31 Jul 2023 v1

posi_conPrismGuide IRD Panel Sequencing Report
Order ID: posi_con
Sample Information
Clinical Sample ID

posi_con

Customer-provided Sample Sex

MaleSequencing Analysis Information
Panel

PrismGuide IRD Panel

Reagent

PrismGuide IRD Panel reagent kit

Analysis Execution Date

31 Jul 2023 14:25:25

On Target Reads (%)

73.86

On And Near Target Reads (%)

82.55

Off Target Reads (%)

17.45

Mapped Reads (%)

99.37

Duplicated Reads (%)

6.33

Reads Mapping Quality 0 (%)

3.53

Average Quality

36.5

Average Insert Size

195.1

Insert size std

55.3

Mean Target Coverage588.33

Targets Not Covered

4

Evenness

83.83

Uniformity

1.573

Derivative Log Ratio Score for PrismGuide IRD Panel
System

0.133

Pipeline-calculated Sample Sex

Male

Low Coverage (>=100x)

98.89

Medium Coverage

65.27

High Coverage

2.14

Data Analysis Information
Analysis Protocol

IRD Protocol v1

Pipeline Version

IRD Pipeline v2.4.3

Enable CNV Calling

Yes

Import SNV Results

Yes

CNV Calling Mode

Yes

Flanking Region (bp)10

Allele Balance Priors Off

YesMinimum Alt Count

5

Minimum Base Quality

20

Minimum Total Read Count

20

Minimum Mapping Quality

30

Max Read Mismatch Fraction

0.04

Threshold for Targets Not Covered

1

Germline Minimum Alt Fraction

0.2

Germline Segmentation p-value Threshold

0.01

Genetic aberration selection criteria (SNV, InDel)

Default SNV Filter

Genetic aberration selection criteria (CNV)

Default CNV Filter

Analysis Program Version

0.3.20SNV/Indel Information
1

Variant (HGVSc)

NM_000350.3:c.5318C>T

Gene Symbol

ABCA4

Variant Type

SNV

Location

1:94014685-94014685

Exon Numbers

38/50

Ref

G

Alt

A

Frequency (Read)

0.53289 (721/1353)

Zygosity

Heterozygous

Amino Acid Change (HGVSp)

NP_000341.2:p.Ala1773Val

User Classification

Pathogenic

ACMG Classification

Pathogenic

ACMG Labels

PS1(ClinVar,HGMD,Custom Variant List),PS3(HGMD,ClinVar),PM2(gnomAD),PP2(ClinVar),PP3(SIFT)

Inheritance Pattern

Recessive

Variant Function

missense_variant

Allele frequency in gnomAD - whole
population

7.557E-5

Allele frequency in gnomAD - East Asian

5.437E-5

1000 Genomes Minor Allele-

Uncontrolled when printed

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SIFT Predictiondeleterious

dbSNP ID

rs760549861

ClinVar ID

236129ClinVar Pathogenicity

Pathogenic/Likely_pathogenic

HGMD

CM087708

GEM-J WGA Allele Frequency

6.586E-5

Report Inclusion

Prioritized, Shortlisted

Variant (HGVSc)

NM_000350.3:c.1760+2T>G

Gene Symbol

ABCA4

Variant Type

SNV

Location

1:94063110-94063110

Exon Numbers

12/50

Ref

A

Alt

C

Frequency (Read)

0.53697 (610/1136)

Zygosity

Heterozygous

Amino Acid Change (HGVSp)-

User Classification

Pathogenic

ACMG Classification

Pathogenic

ACMG Labels

PVS1(VEP),PS3(HGMD),PM2(gnomAD),PP3(dbscSNV),PP5(Pathogenic Variants from PMID:31213501)

Inheritance Pattern

Recessive

Variant Function

splice_donor_variant

Allele frequency in gnomAD - whole
population-

Allele frequency in gnomAD - East Asian-

1000 Genomes Minor Allele-

1000 Genomes Minor Allele Frequency-

SIFT Prediction-

dbSNP ID

rs61751385

ClinVar ID

99076

ClinVar Pathogenicity

Pathogenic

HGMD

CS024002

GEM-J WGA Allele Frequency

6.602E-4

Report Inclusion

Prioritized, Shortlisted

Variant (HGVSc)

NM_000329.3:c.1154C>T

Gene Symbol

RPE65

Variant Type

SNV

Location

1:68431560-68431560

Exon Numbers

11/14

Ref

G

Alt

A

Frequency (Read)

0.53728 (663/1234)

Zygosity

Heterozygous

Amino Acid Change (HGVSp)

NP_000320.1:p.Thr385Met

User Classification

Pathogenic

ACMG Classification

Pathogenic

ACMG Labels

PS1(HGMD),PS3(HGMD),PM2(gnomAD),PP2(ClinVar),PP3(BLOSUM),BP4(SIFT)

Inheritance Pattern

Recessive, DominantVariant Function

missense_variant

Allele frequency in gnomAD - whole
population

2.436E-4

Allele frequency in gnomAD - East Asian

0.002992

1000 Genomes Minor Allele

A

1000 Genomes Minor Allele Frequency

0.0012SIFT Prediction

tolerated

dbSNP ID

rs201379753

ClinVar ID

712719ClinVar Pathogenicity

Conflicting_interpretations_of_pathogenicity

HGMD

CM2015142

GEM-J WGA Allele Frequency

0.005265

Report Inclusion

Prioritized, Shortlisted

Variant (HGVSc)

NM_001034853.2:c.2838_2839delGene Symbol

RPGR

Variant Type

Deletion

Location

X:38286159-38286161

Exon Numbers

15/15

Ref

TCC

Alt

T

Frequency (Read)

0.98675 (149/151)

Zygosity

Hemizygous

Amino Acid Change (HGVSp)

NP_001030025.1:p.Glu947GlyfsTer131

Uncontrolled when printed

2/79

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User Classification

Pathogenic

ACMG Classification

Pathogenic

ACMG Labels

PVS1(VEP),PS3(HGMD,ClinVar),PM2(gnomAD)

Inheritance Pattern

X-linked

Variant Function

frameshift_variant

Allele frequency in gnomAD - whole
population-

Allele frequency in gnomAD - East Asian-

1000 Genomes Minor Allele-

1000 Genomes Minor Allele Frequency-

SIFT Prediction-

dbSNP ID-

ClinVar ID

975119ClinVar Pathogenicity

Pathogenic/Likely_pathogenic

HGMD

CD070505

GEM-J WGA Allele Frequency-

Report Inclusion

Prioritized, Shortlisted

Variant (HGVSc)

NM_025114.4:c.2991+1655A>G

Gene Symbol

CEP290

Variant Type

SNV

Location

12:88101183-88101183

Exon Numbers

Intronic

Ref

T

Alt

C

Frequency (Read)

0.24345 (158/649)

Zygosity

Heterozygous

Amino Acid Change (HGVSp)-

User Classification

Likely pathogenic

ACMG Classification

Likely Pathogenic

ACMG Labels

PS3(HGMD,ClinVar),PM2(gnomAD)

Inheritance Pattern

Recessive

Variant Function

intron_variant

Allele frequency in gnomAD - whole
population-

Allele frequency in gnomAD - East Asian-

1000 Genomes Minor Allele-

1000 Genomes Minor Allele Frequency-

SIFT Prediction-

dbSNP ID

rs281865192

ClinVar ID

1337

ClinVar Pathogenicity

Pathogenic/Likely_pathogenic

HGMD

CS064383

GEM-J WGA Allele Frequency-

Report Inclusion

Prioritized, Shortlisted

Variant (HGVSc)

NM_005183.4:c.1118+6A>G

Gene Symbol

CACNA1F

Variant Type

SNV

Location

X:49228030-49228030

Exon Numbers

Intronic

Ref

T

Alt

C

Frequency (Read)

1.0 (320/320)

Zygosity

Hemizygous

Amino Acid Change (HGVSp)-

User Classification

Uncertain significance

ACMG Classification

Uncertain significance

ACMG Labels

PM2(gnomAD)

Inheritance Pattern

X-linked

Variant Function

splice_donor_region_variant,intron_variant

Allele frequency in gnomAD - whole
population-

Allele frequency in gnomAD - East Asian-

1000 Genomes Minor Allele

C

1000 Genomes Minor Allele Frequency

0.6432SIFT Prediction-

dbSNP ID

rs6609854

ClinVar ID-

ClinVar Pathogenicity

-

HGMD

-

GEM-J WGA Allele Frequency-

Report Inclusion

None

Variant (HGVSc)

NM_006343.3:c.2079+181A>G

Uncontrolled when printed

3/79

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posi_conGene Symbol

MERTK

Variant Type

SNV

Location

2:112010247-112010247

Exon Numbers

Intronic

Ref

A

Alt

G

Frequency (Read)

0.47377 (280/591)

Zygosity

Heterozygous

Amino Acid Change (HGVSp)-

User Classification

Uncertain significance

ACMG Classification

Uncertain significance

ACMG Labels

PM2(gnomAD)

Inheritance Pattern

Recessive

Variant Function

intron_variant

Allele frequency in gnomAD - whole
population-

Allele frequency in gnomAD - East Asian-

1000 Genomes Minor Allele

G

1000 Genomes Minor Allele Frequency

0.2468SIFT Prediction-

dbSNP ID

rs77781750

ClinVar ID-

ClinVar Pathogenicity

-

HGMD

-

GEM-J WGA Allele Frequency

0.117

Report Inclusion

None

Variant (HGVSc)

NM_001375654.1:c.3816C>T

Gene Symbol

RP1

Variant Type

SNV

Location

8:54852653-54852653

Exon Numbers

27/30

Ref

C

Alt

T

Frequency (Read)

0.50265 (284/565)

Zygosity

Heterozygous

Amino Acid Change (HGVSp)

NP_001362583.1:p.Ile1272=

User Classification

Uncertain significance

ACMG Classification

Uncertain significance

ACMG Labels

PM2(gnomAD),BP7(VEP,dbscSNV,GERP)

Inheritance Pattern

Recessive, DominantVariant Functionsynonymous_variant

Allele frequency in gnomAD - whole
population-

Allele frequency in gnomAD - East Asian-

1000 Genomes Minor Allele

T1000 Genomes Minor Allele Frequency

8.0E-4

SIFT Prediction-

dbSNP ID

rs541936347

ClinVar ID-

ClinVar Pathogenicity

-

HGMD

-

GEM-J WGA Allele Frequency-

Report Inclusion

None

Variant (HGVSc)

NM_005183.4:c.3309C>T

Gene Symbol

CACNA1F

Variant Type

SNV

Location

X:49215504-49215504

Exon Numbers

28/48

Ref

G

Alt

A

Frequency (Read)

1.0 (335/335)

Zygosity

Hemizygous

Amino Acid Change (HGVSp)

NP_005174.2:p.His1103=

User Classification

Likely benign

ACMG Classification

Likely Benign

ACMG Labels

PM2(gnomAD),BP6(ClinVar),BP7(VEP,dbscSNV,GERP)

Inheritance Pattern

X-linked

Variant Functionsynonymous_variant

Allele frequency in gnomAD - whole
population-

Allele frequency in gnomAD - East Asian-

1000 Genomes Minor Allele

A

Uncontrolled when printed

4/79

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0.4479SIFT Prediction-

dbSNP ID

rs2075866

ClinVar ID

769231ClinVar Pathogenicity

BenignHGMD-

GEM-J WGA Allele Frequency-

Report Inclusion

None

Variant (HGVSc)

NM_005183.4:c.1842T>C

Gene Symbol

CACNA1F

Variant Type

SNV

Location

X:49224829-49224829

Exon Numbers

14/48

Ref

A

Alt

G

Frequency (Read)

1.0 (433/433)

Zygosity

Hemizygous

Amino Acid Change (HGVSp)

NP_005174.2:p.Gly614=

User Classification

Likely benign

ACMG Classification

Likely Benign

ACMG Labels

PM2(gnomAD),BP6(ClinVar),BP7(VEP,dbscSNV,GERP)

Inheritance Pattern

X-linked

Variant Functionsynonymous_variant

Allele frequency in gnomAD - whole
population-

Allele frequency in gnomAD - East Asian-

1000 Genomes Minor Allele

G

1000 Genomes Minor Allele Frequency

0.5595

SIFT Prediction-

dbSNP ID

rs2235127

ClinVar ID

769230

ClinVar Pathogenicity

BenignHGMD-

GEM-J WGA Allele Frequency-

Report Inclusion

None

Variant (HGVSc)

NM_000260.4:c.2754C>T

Gene Symbol

MYO7A

Variant Type

SNV

Location

11:77181439-77181439

Exon Numbers

23/49

Ref

C

Alt

T

Frequency (Read)

0.50792 (481/947)

Zygosity

Heterozygous

Amino Acid Change (HGVSp)

NP_000251.3:p.Ala918=

User Classification

Likely benign

ACMG Classification

Likely Benign

ACMG Labels

PM2(gnomAD),BS3(ClinVar),BP7(VEP,dbscSNV,GERP)

Inheritance Pattern

Recessive

Variant Functionsynonymous_variant

Allele frequency in gnomAD - whole
population

0.003703

Allele frequency in gnomAD - East Asian

0.01000 Genomes Minor Allele

T1000 Genomes Minor Allele Frequency

0.0086

SIFT Prediction-

dbSNP ID

rs78072361

ClinVar ID

43188

ClinVar Pathogenicity

Benign/Likely_benign

HGMD

-

GEM-J WGA Allele Frequency-

Report Inclusion

None

Variant (HGVSc)

NM_001375654.1:c.2352G>A

Gene Symbol

RP1

Variant Type

SNV

Location

8:54720269-54720269

Exon Numbers

16/30

Ref

G

Alt

A

Frequency (Read)

0.43007 (246/572)

Zygosity

Heterozygous

Amino Acid Change (HGVSp)

NP_001362583.1:p.Lys784=

Uncontrolled when printed

5/79

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User Classification

Likely benign

ACMG Classification

Likely Benign

ACMG Labels

BS1(gnomAD),BP7(VEP,dbscSNV,GERP)

Inheritance Pattern

Recessive, DominantVariant Functionsynonymous_variant

Allele frequency in gnomAD - whole
population

0.01532

Allele frequency in gnomAD - East Asian

0.01000 Genomes Minor Allele

A

1000 Genomes Minor Allele Frequency

0.0232SIFT Prediction-

dbSNP ID

rs76985026

ClinVar ID-

ClinVar Pathogenicity

-

HGMD

-

GEM-J WGA Allele Frequency-

Report Inclusion

None

Variant (HGVSc)

NM_001375654.1:c.3319A>C

Gene Symbol

RP1

Variant Type

SNV

Location

8:54770134-54770134

Exon Numbers

24/30

Ref

A

Alt

C

Frequency (Read)

0.44681 (105/235)

Zygosity

Heterozygous

Amino Acid Change (HGVSp)

NP_001362583.1:p.Asn1107His

User Classification

Likely benign

ACMG Classification

Likely Benign

ACMG Labels

PM2(gnomAD),BP1(ClinVar),BP4(SIFT)

Inheritance Pattern

Recessive, DominantVariant Function

missense_variant

Allele frequency in gnomAD - whole
population-

Allele frequency in gnomAD - East Asian-

1000 Genomes Minor Allele

C

1000 Genomes Minor Allele Frequency

0.0309SIFT Prediction

tolerated

dbSNP ID

rs114997280

ClinVar ID-

ClinVar Pathogenicity

-

HGMD

-

GEM-J WGA Allele Frequency-

Report Inclusion

None

Variant (HGVSc)

NM_178857.6:c.6545C>AGene Symbol

RP1L1

Variant Type

SNV

Location

8:10607553-10607553

Exon Numbers

4/4

Ref

G

Alt

T

Frequency (Read)

0.46746 (395/845)

Zygosity

Heterozygous

Amino Acid Change (HGVSp)

NP_849188.4:p.Ala2182Asp

User Classification

Likely benign

ACMG Classification

Likely Benign

ACMG Labels

PP3(BLOSUM),BS1(gnomAD),BP1(ClinVar),BP4(SIFT),BP6(ClinVar)

Inheritance Pattern

Recessive, DominantVariant Function

missense_variant

Allele frequency in gnomAD - whole
population

0.007286

Allele frequency in gnomAD - East Asian

5.562E-5

1000 Genomes Minor Allele

T1000 Genomes Minor Allele Frequency

0.0038SIFT Prediction

tolerated

dbSNP ID

rs183570817

ClinVar ID

361220

ClinVar Pathogenicity

BenignHGMD-

GEM-J WGA Allele Frequency-

Report Inclusion

None

Variant (HGVSc)

NM_178857.6:c.5837C>A

Uncontrolled when printed

6/79

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RP1L1

Variant Type

SNV

Location

8:10608261-10608261

Exon Numbers

4/4

Ref

G

Alt

T

Frequency (Read)

1.0 (803/803)

Zygosity

Homozygous

Amino Acid Change (HGVSp)

NP_849188.4:p.Ala1946Glu

User Classification

Likely benign

ACMG Classification

Likely Benign

ACMG Labels

PM2(gnomAD),PP3(BLOSUM),BS3(ClinVar),BP1(ClinVar),BP4(SIFT)

Inheritance Pattern

Recessive, DominantVariant Function

missense_variant

Allele frequency in gnomAD - whole
population-

Allele frequency in gnomAD - East Asian-

1000 Genomes Minor Allele

T1000 Genomes Minor Allele Frequency

0.9197

SIFT Prediction

tolerated_low_confidence

dbSNP ID

rs11785822

ClinVar ID

361236

ClinVar Pathogenicity

BenignHGMD-

GEM-J WGA Allele Frequency

0.998

Report Inclusion

None

Variant (HGVSc)

NM_178857.6:c.4019_4020delinsGG

Gene Symbol

RP1L1

Variant Type

MNP

Location

8:10610078-10610079

Exon Numbers

4/4

Ref

TT

Alt

CC

Frequency (Read)

0.27044 (258/954)

Zygosity

Heterozygous

Amino Acid Change (HGVSp)

NP_849188.4:p.Glu1340Gly

User Classification

Likely benign

ACMG Classification

Likely Benign

ACMG Labels

PM2(gnomAD),PP3(BLOSUM),BP1(ClinVar),BP4(SIFT)

Inheritance Pattern

Recessive, DominantVariant Function

missense_variant

Allele frequency in gnomAD - whole
population-

Allele frequency in gnomAD - East Asian-

1000 Genomes Minor Allele-

1000 Genomes Minor Allele Frequency-

SIFT Prediction

tolerated

dbSNP ID

rs1554451516

ClinVar ID-

ClinVar Pathogenicity

-

HGMD

-

GEM-J WGA Allele Frequency-

Report Inclusion

None

Variant (HGVSc)

NM_178857.6:c.3956C>G

Gene Symbol

RP1L1

Variant Type

SNV

Location

8:10610142-10610142

Exon Numbers

4/4

Ref

G

Alt

C

Frequency (Read)

0.87391 (804/920)

Zygosity

Heterozygous

Amino Acid Change (HGVSp)

NP_849188.4:p.Ala1319Gly

User Classification

Likely benign

ACMG Classification

Likely Benign

ACMG Labels

PM2(gnomAD),BS3(ClinVar),BP1(ClinVar),BP4(SIFT),BP6(Benign Variants from PMID:31213501)

Inheritance Pattern

Recessive, DominantVariant Function

missense_variant

Allele frequency in gnomAD - whole
population-

Allele frequency in gnomAD - East Asian-

1000 Genomes Minor Allele-

Uncontrolled when printed

7/79

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SIFT Prediction

tolerated

dbSNP ID

rs4840501

ClinVar ID

361300

ClinVar Pathogenicity

BenignHGMD-

GEM-J WGA Allele Frequency

0.489

Report Inclusion

None

Variant (HGVSc)

NM_022367.4:c.2187G>A

Gene Symbol

SEMA4A

Variant Type

SNV

Location

1:156176898-156176898

Exon Numbers

15/15

Ref

G

Alt

A

Frequency (Read)

0.50693 (439/866)

Zygosity

Heterozygous

Amino Acid Change (HGVSp)

NP_071762.2:p.Pro729=

User Classification

Likely benign

ACMG Classification

Likely Benign

ACMG Labels

BS1(gnomAD),BP7(VEP,dbscSNV,GERP)

Inheritance Pattern

Dominant

Variant Functionsynonymous_variant

Allele frequency in gnomAD - whole
population

0.01542

Allele frequency in gnomAD - East Asian

0.01000 Genomes Minor Allele

A

1000 Genomes Minor Allele Frequency

0.0068SIFT Prediction-

dbSNP ID

rs41265019

ClinVar ID

292858

ClinVar Pathogenicity

Conflicting_interpretations_of_pathogenicity

HGMD

-

GEM-J WGA Allele Frequency-

Report Inclusion

None

Variant (HGVSc)

NM_206933.4:c.1434G>C

Gene Symbol

USH2A

Variant Type

SNV

Location

1:216323590-216323590

Exon Numbers

8/72

Ref

C

Alt

G

Frequency (Read)

0.54383 (304/559)

Zygosity

Heterozygous

Amino Acid Change (HGVSp)

NP_996816.3:p.Glu478Asp

User Classification

Likely benign

ACMG Classification

Likely Benign

ACMG Labels

BS1(gnomAD),BP1(ClinVar),BP4(SIFT)

Inheritance Pattern

Recessive

Variant Function

missense_variant

Allele frequency in gnomAD - whole
population

0.0121Allele frequency in gnomAD - East Asian

0.01000 Genomes Minor Allele

G

1000 Genomes Minor Allele Frequency

0.0048SIFT Prediction

tolerated

dbSNP ID

rs35730265

ClinVar ID

48437

ClinVar Pathogenicity

Conflicting_interpretations_of_pathogenicity

HGMD

-

GEM-J WGA Allele Frequency-

Report Inclusion

None

Variant (HGVSc)

NM_000350.3:c.6764G>T

Gene Symbol

ABCA4

Variant Type

SNV

Location

1:93996161-93996161

Exon Numbers

49/50

Ref

C

Alt

A

Frequency (Read)

0.52402 (349/666)

Zygosity

Heterozygous

Amino Acid Change (HGVSp)

NP_000341.2:p.Ser2255Ile

Uncontrolled when printed

8/79

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User Classification

BenignACMG Classification

BenignACMG Labels

PP2(ClinVar),PP3(BLOSUM),BA1(gnomAD),BS1(gnomAD),BS3(ClinVar),BP4(SIFT)

Inheritance Pattern

Recessive

Variant Function

missense_variant

Allele frequency in gnomAD - whole
population

0.07149

Allele frequency in gnomAD - East Asian

0.02702

1000 Genomes Minor Allele

A

1000 Genomes Minor Allele Frequency

0.1769SIFT Prediction

tolerated

dbSNP ID

rs6666652

ClinVar ID

99494

ClinVar Pathogenicity

BenignHGMD-

GEM-J WGA Allele Frequency

0.019

Report Inclusion

None

Variant (HGVSc)

NM_000350.3:c.6730-3T>C

Gene Symbol

ABCA4

Variant Type

SNV

Location

1:93996198-93996198

Exon Numbers

Intronic

Ref

A

Alt

G

Frequency (Read)

0.53008 (282/532)

Zygosity

Heterozygous

Amino Acid Change (HGVSp)-

User Classification

BenignACMG Classification

BenignACMG Labels

BA1(gnomAD),BS1(gnomAD),BS3(ClinVar),BP4(dbscSNV),BP6(Benign Variants from PMID:31213501)

Inheritance Pattern

Recessive

Variant Function

splice_polypyrimidine_tract_variant,splice_region_variant,intron_variant

Allele frequency in gnomAD - whole
population

0.06522

Allele frequency in gnomAD - East Asian

0.02703

1000 Genomes Minor Allele

G

1000 Genomes Minor Allele Frequency

0.1486

SIFT Prediction-

dbSNP ID

rs1800717

ClinVar ID

99491

ClinVar Pathogenicity

BenignHGMD-

GEM-J WGA Allele Frequency

0.019

Report Inclusion

None

Variant (HGVSc)

NM_000350.3:c.6285T>C

Gene Symbol

ABCA4

Variant Type

SNV

Location

1:94001103-94001103

Exon Numbers

46/50

Ref

A

Alt

G

Frequency (Read)

0.48544 (250/515)

Zygosity

Heterozygous

Amino Acid Change (HGVSp)

NP_000341.2:p.Asp2095=

User Classification

BenignACMG Classification

BenignACMG Labels

BA1(gnomAD),BS1(gnomAD),BS3(ClinVar),BP7(VEP,dbscSNV,GERP)

Inheritance Pattern

Recessive

Variant Function

splice_region_variant,synonymous_variant

Allele frequency in gnomAD - whole
population

0.1578Allele frequency in gnomAD - East Asian

0.14861000 Genomes Minor Allele

G

1000 Genomes Minor Allele Frequency

0.3011

SIFT Prediction-

dbSNP ID

rs1801555

ClinVar ID

99444

ClinVar Pathogenicity

BenignHGMD-

GEM-J WGA Allele Frequency

0.144

Report Inclusion

None

Variant (HGVSc)

NM_000350.3:c.6282+7G>A

Uncontrolled when printed

9/79

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posi_conGene Symbol

ABCA4

Variant Type

SNV

Location

1:94001851-94001851

Exon Numbers

Intronic

Ref

C

Alt

T

Frequency (Read)

0.49858 (350/702)

Zygosity

Heterozygous

Amino Acid Change (HGVSp)-

User Classification

BenignACMG Classification

BenignACMG Labels

BA1(gnomAD),BS1(gnomAD),BS3(ClinVar),BP4(dbscSNV)

Inheritance Pattern

Recessive

Variant Function

splice_region_variant,intron_variant

Allele frequency in gnomAD - whole
population

0.0766

Allele frequency in gnomAD - East Asian

0.06161

1000 Genomes Minor Allele

T1000 Genomes Minor Allele Frequency

0.134

SIFT Prediction-

dbSNP ID

rs17110761

ClinVar ID

99443

ClinVar Pathogenicity

Benign/Likely_benign

HGMD

-

GEM-J WGA Allele Frequency

0.041

Report Inclusion

None

Variant (HGVSc)

NM_000350.3:c.6249C>T

Gene Symbol

ABCA4

Variant Type

SNV

Location

1:94001891-94001891

Exon Numbers

45/50

Ref

G

Alt

A

Frequency (Read)

0.53635 (450/839)

Zygosity

Heterozygous

Amino Acid Change (HGVSp)

NP_000341.2:p.Ile2083=

User Classification

BenignACMG Classification

BenignACMG Labels

BA1(gnomAD),BS1(gnomAD),BS3(ClinVar),BP7(VEP,dbscSNV,GERP)

Inheritance Pattern

Recessive

Variant Functionsynonymous_variant

Allele frequency in gnomAD - whole
population

0.07668

Allele frequency in gnomAD - East Asian

0.061451000 Genomes Minor Allele

A

1000 Genomes Minor Allele Frequency

0.134

SIFT Prediction-

dbSNP ID

rs1801359

ClinVar ID

99440

ClinVar Pathogenicity

Benign/Likely_benign

HGMD

-

GEM-J WGA Allele Frequency

0.041

Report Inclusion

None

Variant (HGVSc)

NM_000350.3:c.6069T>C

Gene Symbol

ABCA4

Variant Type

SNV

Location

1:94005519-94005519

Exon Numbers

44/50

Ref

A

Alt

G

Frequency (Read)

0.45991 (304/661)

Zygosity

Heterozygous

Amino Acid Change (HGVSp)

NP_000341.2:p.Ile2023=

User Classification

BenignACMG Classification

BenignACMG Labels

BA1(gnomAD),BS1(gnomAD),BS3(ClinVar),BP7(VEP,dbscSNV,GERP)

Inheritance Pattern

Recessive

Variant Functionsynonymous_variant

Allele frequency in gnomAD - whole
population

0.8979Allele frequency in gnomAD - East Asian

0.88521000 Genomes Minor Allele

G

Uncontrolled when printed

10/79

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27

28

posi_con1000 Genomes Minor Allele Frequency

0.77

SIFT Prediction-

dbSNP ID

rs1762114

ClinVar ID

136235

ClinVar Pathogenicity

BenignHGMD-

GEM-J WGA Allele Frequency

0.925

Report Inclusion

None

Variant (HGVSc)

NM_000350.3:c.635G>A

Gene Symbol

ABCA4

Variant Type

SNV

Location

1:94098927-94098927

Exon Numbers

6/50

Ref

C

Alt

T

Frequency (Read)

0.44207 (393/889)

Zygosity

Heterozygous

Amino Acid Change (HGVSp)

NP_000341.2:p.Arg212His

User Classification

BenignACMG Classification

BenignACMG Labels

PM5(ClinVar),PP2(ClinVar),PP3(SIFT),BS1(gnomAD),BS3(ClinVar),BP6(Benign Variants from PMID:31213501)

Inheritance Pattern

Recessive

Variant Function

missense_variant

Allele frequency in gnomAD - whole
population

0.04109

Allele frequency in gnomAD - East Asian

0.06135

1000 Genomes Minor Allele

T1000 Genomes Minor Allele Frequency

0.0533

SIFT Predictiondeleterious

dbSNP ID

rs6657239

ClinVar ID

99454

ClinVar Pathogenicity

Benign/Likely_benign

HGMD

-

GEM-J WGA Allele Frequency

0.059

Report Inclusion

None

Variant (HGVSc)

NM_000350.3:c.141A>G

Gene Symbol

ABCA4

Variant Type

SNV

Location

1:94112992-94112992

Exon Numbers

2/50

Ref

T

Alt

C

Frequency (Read)

1.0 (618/618)

Zygosity

Homozygous

Amino Acid Change (HGVSp)

NP_000341.2:p.Pro47=

User Classification

BenignACMG Classification

BenignACMG Labels

BA1(gnomAD),BS1(gnomAD),BS3(ClinVar),BP7(VEP,dbscSNV,GERP)

Inheritance Pattern

Recessive

Variant Functionsynonymous_variant

Allele frequency in gnomAD - whole
population

0.9971Allele frequency in gnomAD - East Asian

0.99991000 Genomes Minor Allele

C

1000 Genomes Minor Allele Frequency

0.987

SIFT Prediction-

dbSNP ID

rs4847281

ClinVar ID

166618

ClinVar Pathogenicity

BenignHGMD-

GEM-J WGA Allele Frequency

1.0

Report Inclusion

None

Variant (HGVSc)

NM_032119.4:c.2367+8C>T

Gene Symbol

ADGRV1

Variant Type

SNV

Location

5:90642770-90642770

Exon Numbers

Intronic

Ref

C

Alt

T

Frequency (Read)

0.49622 (197/397)

Zygosity

Heterozygous

Amino Acid Change (HGVSp)-

Uncontrolled when printed

11/79

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31

posi_con

User Classification

BenignACMG Classification

BenignACMG Labels

BA1(gnomAD),BS1(gnomAD),BS3(ClinVar),BP4(dbscSNV)

Inheritance Pattern

Recessive

Variant Function

splice_region_variant,intron_variant

Allele frequency in gnomAD - whole
population

0.7328Allele frequency in gnomAD - East Asian

0.80721000 Genomes Minor Allele

T1000 Genomes Minor Allele Frequency

0.8213

SIFT Prediction-

dbSNP ID

rs2366773

ClinVar ID

46305

ClinVar Pathogenicity

BenignHGMD-

GEM-J WGA Allele Frequency

0.837

Report Inclusion

None

Variant (HGVSc)

NM_032119.4:c.3279G>T

Gene Symbol

ADGRV1

Variant Type

SNV

Location

5:90647754-90647754

Exon Numbers

17/90

Ref

G

Alt

T

Frequency (Read)

0.42105 (184/437)

Zygosity

Heterozygous

Amino Acid Change (HGVSp)

NP_115495.3:p.Leu1093Phe

User Classification

BenignACMG Classification

BenignACMG Labels

BA1(gnomAD),BS1(gnomAD),BS3(ClinVar),BP1(ClinVar),BP4(SIFT)

Inheritance Pattern

Recessive

Variant Function

missense_variant

Allele frequency in gnomAD - whole
population

0.7114

Allele frequency in gnomAD - East Asian

0.80141000 Genomes Minor Allele

T1000 Genomes Minor Allele Frequency

0.8103

SIFT Prediction

tolerated

dbSNP ID

rs2366777

ClinVar ID

46313

ClinVar Pathogenicity

BenignHGMD-

GEM-J WGA Allele Frequency

0.833

Report Inclusion

None

Variant (HGVSc)

NM_032119.4:c.5851G>A

Gene Symbol

ADGRV1

Variant Type

SNV

Location

5:90683772-90683772

Exon Numbers

28/90

Ref

G

Alt

A

Frequency (Read)

0.49228 (319/648)

Zygosity

Heterozygous

Amino Acid Change (HGVSp)

NP_115495.3:p.Val1951Ile

User Classification

BenignACMG Classification

BenignACMG Labels

BA1(gnomAD),BS1(gnomAD),BS3(ClinVar),BP1(ClinVar),BP4(SIFT)

Inheritance Pattern

Recessive

Variant Function

missense_variant

Allele frequency in gnomAD - whole
population

0.7096

Allele frequency in gnomAD - East Asian

0.80071000 Genomes Minor Allele

A

1000 Genomes Minor Allele Frequency

0.8037

SIFT Prediction

tolerated

dbSNP ID

rs4916684

ClinVar ID

46343

ClinVar Pathogenicity

BenignHGMD-

GEM-J WGA Allele Frequency

0.836

Report Inclusion

None

Variant (HGVSc)

NM_032119.4:c.5960C>T

Uncontrolled when printed

12/79

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posi_conGene Symbol

ADGRV1

Variant Type

SNV

Location

5:90683881-90683881

Exon Numbers

28/90

Ref

C

Alt

T

Frequency (Read)

0.51495 (310/602)

Zygosity

Heterozygous

Amino Acid Change (HGVSp)

NP_115495.3:p.Pro1987Leu

User Classification

BenignACMG Classification

BenignACMG Labels

PP3(BLOSUM),BA1(gnomAD),BS1(gnomAD),BS3(ClinVar),BP1(ClinVar),BP4(SIFT)

Inheritance Pattern

Recessive

Variant Function

missense_variant

Allele frequency in gnomAD - whole
population

0.3639Allele frequency in gnomAD - East Asian

0.36921000 Genomes Minor Allele

T1000 Genomes Minor Allele Frequency

0.3373

SIFT Prediction

tolerated

dbSNP ID

rs4916685

ClinVar ID

46345

ClinVar Pathogenicity

BenignHGMD-

GEM-J WGA Allele Frequency

0.486

Report Inclusion

None

Variant (HGVSc)

NM_032119.4:c.6695A>G

Gene Symbol

ADGRV1

Variant Type

SNV

Location

5:90690065-90690065

Exon Numbers

30/90

Ref

A

Alt

G

Frequency (Read)

0.45243 (214/473)

Zygosity

Heterozygous

Amino Acid Change (HGVSp)

NP_115495.3:p.Tyr2232Cys

User Classification

BenignACMG Classification

BenignACMG Labels

PP3(SIFT),BA1(gnomAD),BS1(gnomAD),BS3(ClinVar),BP1(ClinVar)

Inheritance Pattern

Recessive

Variant Function

missense_variant

Allele frequency in gnomAD - whole
population

0.3647

Allele frequency in gnomAD - East Asian

0.36531000 Genomes Minor Allele

G

1000 Genomes Minor Allele Frequency

0.3498SIFT Predictiondeleterious

dbSNP ID

rs10037067

ClinVar ID

46356

ClinVar Pathogenicity

BenignHGMD-

GEM-J WGA Allele Frequency

0.486

Report Inclusion

None

Variant (HGVSc)

NM_032119.4:c.6952-10G>A

Gene Symbol

ADGRV1

Variant Type

SNV

Location

5:90692595-90692595

Exon Numbers

Intronic

Ref

G

Alt

A

Frequency (Read)

0.44474 (165/371)

Zygosity

Heterozygous

Amino Acid Change (HGVSp)-

User Classification

BenignACMG Classification

BenignACMG Labels

BA1(gnomAD),BS1(gnomAD),BS3(ClinVar)

Inheritance Pattern

Recessive

Variant Function

splice_polypyrimidine_tract_variant,intron_variant

Allele frequency in gnomAD - whole
population

0.3479Allele frequency in gnomAD - East Asian

0.36081000 Genomes Minor Allele

A

Uncontrolled when printed

13/79

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36

posi_con1000 Genomes Minor Allele Frequency

0.3221

SIFT Prediction-

dbSNP ID

rs10040165

ClinVar ID

46358

ClinVar Pathogenicity

BenignHGMD-

GEM-J WGA Allele Frequency

0.486

Report Inclusion

None

Variant (HGVSc)

NM_032119.4:c.7034A>G

Gene Symbol

ADGRV1

Variant Type

SNV

Location

5:90692687-90692687

Exon Numbers

32/90

Ref

A

Alt

G

Frequency (Read)

0.46281 (280/605)

Zygosity

Heterozygous

Amino Acid Change (HGVSp)

NP_115495.3:p.Asn2345Ser

User Classification

BenignACMG Classification

BenignACMG Labels

BA1(gnomAD),BS1(gnomAD),BS3(ClinVar),BP1(ClinVar),BP4(SIFT)

Inheritance Pattern

Recessive

Variant Function

missense_variant

Allele frequency in gnomAD - whole
population

0.3581Allele frequency in gnomAD - East Asian

0.3691000 Genomes Minor Allele

G

1000 Genomes Minor Allele Frequency

0.3223

SIFT Prediction

tolerated

dbSNP ID

rs2366926

ClinVar ID

46360

ClinVar Pathogenicity

BenignHGMD-

GEM-J WGA Allele Frequency

0.487

Report Inclusion

None

Variant (HGVSc)

NM_032119.4:c.7206G>A

Gene Symbol

ADGRV1

Variant Type

SNV

Location

5:90693962-90693962

Exon Numbers

33/90

Ref

G

Alt

A

Frequency (Read)

0.49849 (331/664)

Zygosity

Heterozygous

Amino Acid Change (HGVSp)

NP_115495.3:p.Glu2402=

User Classification

BenignACMG Classification

BenignACMG Labels

BA1(gnomAD),BS1(gnomAD),BS3(ClinVar),BP7(VEP,dbscSNV,GERP)

Inheritance Pattern

Recessive

Variant Functionsynonymous_variant

Allele frequency in gnomAD - whole
population

0.3596

Allele frequency in gnomAD - East Asian

0.36811000 Genomes Minor Allele

A

1000 Genomes Minor Allele Frequency

0.3221

SIFT Prediction-

dbSNP ID

rs16876822

ClinVar ID

46365

ClinVar Pathogenicity

BenignHGMD-

GEM-J WGA Allele Frequency

0.486

Report Inclusion

None

Variant (HGVSc)

NM_032119.4:c.7751A>G

Gene Symbol

ADGRV1

Variant Type

SNV

Location

5:90694507-90694507

Exon Numbers

33/90

Ref

A

Alt

G

Frequency (Read)

0.45847 (287/626)

Zygosity

Heterozygous

Amino Acid Change (HGVSp)

NP_115495.3:p.Asn2584Ser

Uncontrolled when printed

14/79

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posi_con

User Classification

BenignACMG Classification

BenignACMG Labels

BA1(gnomAD),BS1(gnomAD),BS3(ClinVar),BP1(ClinVar),BP4(SIFT)

Inheritance Pattern

Recessive

Variant Function

missense_variant

Allele frequency in gnomAD - whole
population

0.7107

Allele frequency in gnomAD - East Asian

0.80061000 Genomes Minor Allele

G

1000 Genomes Minor Allele Frequency

0.8085

SIFT Prediction

tolerated

dbSNP ID

rs1878878

ClinVar ID

46379

ClinVar Pathogenicity

BenignHGMD-

GEM-J WGA Allele Frequency

0.836

Report Inclusion

None

Variant (HGVSc)

NM_032119.4:c.8730+21dup

Gene Symbol

ADGRV1

Variant TypeInsertion

Location

5:90706403-90706403

Exon Numbers

Intronic

Ref

C

Alt

CT

Frequency (Read)

0.36777 (89/242)

Zygosity

Heterozygous

Amino Acid Change (HGVSp)-

User Classification

BenignACMG Classification

BenignACMG Labels

BA1(gnomAD),BS1(gnomAD),BS3(ClinVar)

Inheritance Pattern

Recessive

Variant Function

intron_variant

Allele frequency in gnomAD - whole
population

0.4707

Allele frequency in gnomAD - East Asian

0.49161000 Genomes Minor Allele-

1000 Genomes Minor Allele Frequency-

SIFT Prediction-

dbSNP ID

rs60522638

ClinVar ID

197047

ClinVar Pathogenicity

Benign/Likely_benign

HGMD

-

GEM-J WGA Allele Frequency

0.756

Report Inclusion

None

Variant (HGVSc)

NM_032119.4:c.9927T>G

Gene Symbol

ADGRV1

Variant Type

SNV

Location

5:90725106-90725106

Exon Numbers

47/90

Ref

T

Alt

G

Frequency (Read)

0.49451 (90/182)

Zygosity

Heterozygous

Amino Acid Change (HGVSp)

NP_115495.3:p.Pro3309=

User Classification

BenignACMG Classification

BenignACMG Labels

BA1(gnomAD),BS1(gnomAD),BS3(ClinVar),BP7(VEP,dbscSNV,GERP)

Inheritance Pattern

Recessive

Variant Functionsynonymous_variant

Allele frequency in gnomAD - whole
population

0.3459Allele frequency in gnomAD - East Asian

0.36651000 Genomes Minor Allele-

1000 Genomes Minor Allele Frequency-

SIFT Prediction-

dbSNP ID

rs16869042

ClinVar ID

46409

ClinVar Pathogenicity

BenignHGMD-

GEM-J WGA Allele Frequency

0.488

Report Inclusion

None

Variant (HGVSc)

NM_032119.4:c.10411G>A

Uncontrolled when printed

15/79

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posi_conGene Symbol

ADGRV1

Variant Type

SNV

Location

5:90728918-90728918

Exon Numbers

49/90

Ref

G

Alt

A

Frequency (Read)

0.5045 (168/333)

Zygosity

Heterozygous

Amino Acid Change (HGVSp)

NP_115495.3:p.Glu3471Lys

User Classification

BenignACMG Classification

BenignACMG Labels

BA1(gnomAD),BS1(gnomAD),BS3(ClinVar),BP1(ClinVar),BP4(SIFT)

Inheritance Pattern

Recessive

Variant Function

missense_variant

Allele frequency in gnomAD - whole
population

0.75

Allele frequency in gnomAD - East Asian

0.78461000 Genomes Minor Allele

A

1000 Genomes Minor Allele Frequency

0.8291

SIFT Prediction

tolerated

dbSNP ID

rs2366928

ClinVar ID

46248

ClinVar Pathogenicity

BenignHGMD-

GEM-J WGA Allele Frequency

0.821

Report Inclusion

None

Variant (HGVSc)

NM_032119.4:c.10872A>G

Gene Symbol

ADGRV1

Variant Type

SNV

Location

5:90745693-90745693

Exon Numbers

52/90

Ref

A

Alt

G

Frequency (Read)

0.40892 (220/538)

Zygosity

Heterozygous

Amino Acid Change (HGVSp)

NP_115495.3:p.Gln3624=

User Classification

BenignACMG Classification

BenignACMG Labels

BS1(gnomAD),BS3(ClinVar),BP7(VEP,dbscSNV,GERP)

Inheritance Pattern

Recessive

Variant Functionsynonymous_variant

Allele frequency in gnomAD - whole
population

0.03118

Allele frequency in gnomAD - East Asian

5.572E-5

1000 Genomes Minor Allele

G

1000 Genomes Minor Allele Frequency

0.0174

SIFT Prediction-

dbSNP ID

rs17624033

ClinVar ID

46252

ClinVar Pathogenicity

BenignHGMD-

GEM-J WGA Allele Frequency-

Report Inclusion

None

Variant (HGVSc)

NM_032119.4:c.11581-3dup

Gene Symbol

ADGRV1

Variant TypeInsertion

Location

5:90756446-90756446

Exon Numbers

Intronic

Ref

T

Alt

TC

Frequency (Read)

0.43778 (197/450)

Zygosity

Heterozygous

Amino Acid Change (HGVSp)-

User Classification

BenignACMG Classification

BenignACMG Labels

BA1(gnomAD),BS1(gnomAD),BS3(ClinVar)

Inheritance Pattern

Recessive

Variant Function

splice_polypyrimidine_tract_variant,splice_region_variant,intron_variant

Allele frequency in gnomAD - whole
population

0.4024

Allele frequency in gnomAD - East Asian

0.40741000 Genomes Minor Allele

C

Uncontrolled when printed

16/79

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43

44

posi_con1000 Genomes Minor Allele Frequency

0.3852SIFT Prediction-

dbSNP ID

rs34894132

ClinVar ID

46256

ClinVar Pathogenicity

BenignHGMD-

GEM-J WGA Allele Frequency

0.551

Report Inclusion

None

Variant (HGVSc)

NM_032119.4:c.11599G>A

Gene Symbol

ADGRV1

Variant Type

SNV

Location

5:90756472-90756472

Exon Numbers

56/90

Ref

G

Alt

A

Frequency (Read)

0.47312 (264/558)

Zygosity

Heterozygous

Amino Acid Change (HGVSp)

NP_115495.3:p.Glu3867Lys

User Classification

BenignACMG Classification

BenignACMG Labels

BA1(gnomAD),BS1(gnomAD),BS3(ClinVar),BP1(ClinVar),BP4(SIFT)

Inheritance Pattern

Recessive

Variant Function

missense_variant

Allele frequency in gnomAD - whole
population

0.3439Allele frequency in gnomAD - East Asian

0.43331000 Genomes Minor Allele

A

1000 Genomes Minor Allele Frequency

0.2961

SIFT Prediction

tolerated

dbSNP ID

rs10062026

ClinVar ID

46257

ClinVar Pathogenicity

BenignHGMD-

GEM-J WGA Allele Frequency

0.551

Report Inclusion

None

Variant (HGVSc)

NM_032119.4:c.11682C>T

Gene Symbol

ADGRV1

Variant Type

SNV

Location

5:90756555-90756555

Exon Numbers

56/90

Ref

C

Alt

T

Frequency (Read)

0.4538 (275/606)

Zygosity

Heterozygous

Amino Acid Change (HGVSp)

NP_115495.3:p.Pro3894=

User Classification

BenignACMG Classification

BenignACMG Labels

BA1(gnomAD),BS1(gnomAD),BS3(ClinVar),BP7(VEP,dbscSNV,GERP)

Inheritance Pattern

Recessive

Variant Functionsynonymous_variant

Allele frequency in gnomAD - whole
population

0.4868Allele frequency in gnomAD - East Asian

0.45561000 Genomes Minor Allele

T1000 Genomes Minor Allele Frequency

0.5393

SIFT Prediction-

dbSNP ID

rs2438349

ClinVar ID

46258

ClinVar Pathogenicity

BenignHGMD-

GEM-J WGA Allele Frequency

0.552

Report Inclusion

None

Variant (HGVSc)

NM_032119.4:c.16031A>G

Gene Symbol

ADGRV1

Variant Type

SNV

Location

5:90811291-90811291

Exon Numbers

74/90

Ref

A

Alt

G

Frequency (Read)

0.99821 (558/559)

Zygosity

Homozygous

Amino Acid Change (HGVSp)

NP_115495.3:p.Glu5344Gly

Uncontrolled when printed

17/79

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47

posi_con

User Classification

BenignACMG Classification

BenignACMG Labels

PP3(BLOSUM),BA1(gnomAD),BS1(gnomAD),BS3(ClinVar),BP1(ClinVar),BP4(SIFT)

Inheritance Pattern

Recessive

Variant Function

missense_variant

Allele frequency in gnomAD - whole
population

0.9696

Allele frequency in gnomAD - East Asian

1.01000 Genomes Minor Allele

G

1000 Genomes Minor Allele Frequency

0.9461

SIFT Prediction

tolerated

dbSNP ID

rs2438374

ClinVar ID

46282

ClinVar Pathogenicity

BenignHGMD-

GEM-J WGA Allele Frequency

1.0

Report Inclusion

None

Variant (HGVSc)

NM_032119.4:c.16279G>A

Gene Symbol

ADGRV1

Variant Type

SNV

Location

5:90823507-90823507

Exon Numbers

76/90

Ref

G

Alt

A

Frequency (Read)

1.0 (684/684)

Zygosity

Homozygous

Amino Acid Change (HGVSp)

NP_115495.3:p.Val5427Met

User Classification

BenignACMG Classification

BenignACMG Labels

BA1(gnomAD),BS1(gnomAD),BS3(ClinVar),BP1(ClinVar),BP4(SIFT)

Inheritance Pattern

Recessive

Variant Function

missense_variant

Allele frequency in gnomAD - whole
population

0.9931Allele frequency in gnomAD - East Asian

1.01000 Genomes Minor Allele

A

1000 Genomes Minor Allele Frequency

0.9722SIFT Prediction

tolerated

dbSNP ID

rs2438378

ClinVar ID

46285

ClinVar Pathogenicity

BenignHGMD-

GEM-J WGA Allele Frequency

1.0

Report Inclusion

None

Variant (HGVSc)

NM_032119.4:c.18625-7T>C

Gene Symbol

ADGRV1

Variant Type

SNV

Location

5:91153214-91153214

Exon Numbers

Intronic

Ref

T

Alt

C

Frequency (Read)

1.0 (555/555)

Zygosity

Homozygous

Amino Acid Change (HGVSp)-

User Classification

BenignACMG Classification

BenignACMG Labels

BA1(gnomAD),BS1(gnomAD),BS3(ClinVar),BP4(dbscSNV)

Inheritance Pattern

Recessive

Variant Function

splice_polypyrimidine_tract_variant,splice_region_variant,intron_variant

Allele frequency in gnomAD - whole
population

0.925

Allele frequency in gnomAD - East Asian

0.89491000 Genomes Minor Allele

C

1000 Genomes Minor Allele Frequency

0.8984

SIFT Prediction-

dbSNP ID

rs7726023

ClinVar ID

46299

ClinVar Pathogenicity

BenignHGMD-

GEM-J WGA Allele Frequency

0.862

Report Inclusion

None

Variant (HGVSc)

NM_004183.4:c.109T>C

Uncontrolled when printed

18/79

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posi_conGene Symbol

BEST1

Variant Type

SNV

Location

11:61951915-61951915

Exon Numbers

2/11

Ref

T

Alt

C

Frequency (Read)

0.48972 (405/827)

Zygosity

Heterozygous

Amino Acid Change (HGVSp)

NP_004174.1:p.Leu37=

User Classification

BenignACMG Classification

BenignACMG Labels

BA1(gnomAD),BS1(gnomAD),BS3(ClinVar),BP7(VEP,dbscSNV,GERP)

Inheritance Pattern

Recessive, DominantVariant Functionsynonymous_variant

Allele frequency in gnomAD - whole
population

0.4877

Allele frequency in gnomAD - East Asian

0.9121000 Genomes Minor Allele

C

1000 Genomes Minor Allele Frequency

0.6805

SIFT Prediction-

dbSNP ID

rs1800007

ClinVar ID

99678

ClinVar Pathogenicity

BenignHGMD-

GEM-J WGA Allele Frequency

0.956

Report Inclusion

None

Variant (HGVSc)

NM_004183.4:c.1410G>A

Gene Symbol

BEST1

Variant Type

SNV

Location

11:61962564-61962564

Exon Numbers

10/11

Ref

G

Alt

A

Frequency (Read)

0.52189 (441/845)

Zygosity

Heterozygous

Amino Acid Change (HGVSp)

NP_004174.1:p.Thr470=

User Classification

BenignACMG Classification

BenignACMG Labels

BA1(gnomAD),BS1(gnomAD),BS3(ClinVar),BP7(VEP,dbscSNV,GERP)

Inheritance Pattern

Recessive, DominantVariant Functionsynonymous_variant

Allele frequency in gnomAD - whole
population

0.2263

Allele frequency in gnomAD - East Asian

0.001907

1000 Genomes Minor Allele

A

1000 Genomes Minor Allele Frequency

0.1122SIFT Prediction-

dbSNP ID

rs149698

ClinVar ID

193666

ClinVar Pathogenicity

BenignHGMD-

GEM-J WGA Allele Frequency

5.318E-4

Report Inclusion

None

Variant (HGVSc)

NM_004183.4:c.1557C>T

Gene Symbol

BEST1

Variant Type

SNV

Location

11:61962711-61962711

Exon Numbers

10/11

Ref

C

Alt

T

Frequency (Read)

0.51945 (414/797)

Zygosity

Heterozygous

Amino Acid Change (HGVSp)

NP_004174.1:p.Ser519=

User Classification

BenignACMG Classification

BenignACMG Labels

BA1(gnomAD),BS1(gnomAD),BS3(ClinVar),BP7(VEP,dbscSNV,GERP)

Inheritance Pattern

Recessive, DominantVariant Functionsynonymous_variant

Allele frequency in gnomAD - whole
population

0.1748Allele frequency in gnomAD - East Asian

0.001253

1000 Genomes Minor Allele

T

Uncontrolled when printed

19/79

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52

posi_con1000 Genomes Minor Allele Frequency

0.1014

SIFT Prediction-

dbSNP ID

rs1800008

ClinVar ID

99680

ClinVar Pathogenicity

BenignHGMD-

GEM-J WGA Allele Frequency

2.643E-4

Report Inclusion

None

Variant (HGVSc)

NM_004183.4:c.1608T>C

Gene Symbol

BEST1

Variant Type

SNV

Location

11:61962762-61962762

Exon Numbers

10/11

Ref

T

Alt

C

Frequency (Read)

0.50532 (380/752)

Zygosity

Heterozygous

Amino Acid Change (HGVSp)

NP_004174.1:p.Thr536=

User Classification

BenignACMG Classification

BenignACMG Labels

BA1(gnomAD),BS1(gnomAD),BS3(ClinVar),BP7(VEP,dbscSNV,GERP)

Inheritance Pattern

Recessive, DominantVariant Functionsynonymous_variant

Allele frequency in gnomAD - whole
population

0.4599Allele frequency in gnomAD - East Asian

0.86071000 Genomes Minor Allele

C

1000 Genomes Minor Allele Frequency

0.5915

SIFT Prediction-

dbSNP ID

rs1800009

ClinVar ID

99682

ClinVar Pathogenicity

BenignHGMD-

GEM-J WGA Allele Frequency

0.941

Report Inclusion

None

Variant (HGVSc)

NM_004183.4:c.1739+188T>C

Gene Symbol

BEST1

Variant Type

SNV

Location

11:61963081-61963081

Exon Numbers

Intronic

Ref

T

Alt

C

Frequency (Read)

0.50248 (405/806)

Zygosity

Heterozygous

Amino Acid Change (HGVSp)-

User Classification

BenignACMG Classification

BenignACMG Labels

BA1(gnomAD),BS1(gnomAD),BP6(ClinVar)

Inheritance Pattern

Recessive, DominantVariant Function

intron_variant

Allele frequency in gnomAD - whole
population

0.178

Allele frequency in gnomAD - East Asian

0.003559

1000 Genomes Minor Allele

C

1000 Genomes Minor Allele Frequency

0.1044

SIFT Prediction-

dbSNP ID

rs17185413

ClinVar ID

1277400

ClinVar Pathogenicity

BenignHGMD-

GEM-J WGA Allele Frequency

1.98E-4

Report Inclusion

None

Variant (HGVSc)

NM_022124.6:c.366T>C

Gene Symbol

CDH23

Variant Type

SNV

Location

10:71511149-71511149

Exon Numbers

6/70

Ref

T

Alt

C

Frequency (Read)

0.52393 (405/773)

Zygosity

Heterozygous

Amino Acid Change (HGVSp)

NP_071407.4:p.Val122=

Uncontrolled when printed

20/79

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55

posi_con

User Classification

BenignACMG Classification

BenignACMG Labels

BA1(gnomAD),BS1(gnomAD),BS3(ClinVar),BP7(VEP,dbscSNV,GERP)

Inheritance Pattern

Recessive

Variant Functionsynonymous_variant

Allele frequency in gnomAD - whole
population

0.6614

Allele frequency in gnomAD - East Asian

0.77831000 Genomes Minor Allele

C

1000 Genomes Minor Allele Frequency

0.7346

SIFT Prediction-

dbSNP ID

rs3802720

ClinVar ID

45928

ClinVar Pathogenicity

BenignHGMD-

GEM-J WGA Allele Frequency

0.742

Report Inclusion

None

Variant (HGVSc)

NM_022124.6:c.1449+130T>C

Gene Symbol

CDH23

Variant Type

SNV

Location

10:71646747-71646747

Exon Numbers

Intronic

Ref

T

Alt

C

Frequency (Read)

0.49706 (338/680)

Zygosity

Heterozygous

Amino Acid Change (HGVSp)-

User Classification

BenignACMG Classification

BenignACMG Labels

BA1(gnomAD),BS1(gnomAD),BS3(ClinVar)

Inheritance Pattern

Recessive

Variant Function

intron_variant

Allele frequency in gnomAD - whole
population

0.1436

Allele frequency in gnomAD - East Asian

0.07479

1000 Genomes Minor Allele

C

1000 Genomes Minor Allele Frequency

0.1206

SIFT Prediction-

dbSNP ID

rs2305209

ClinVar ID

45870

ClinVar Pathogenicity

BenignHGMD-

GEM-J WGA Allele Frequency

0.081

Report Inclusion

None

Variant (HGVSc)

NM_022124.6:c.1487G>A

Gene Symbol

CDH23

Variant Type

SNV

Location

10:71675149-71675149

Exon Numbers

15/70

Ref

G

Alt

A

Frequency (Read)

0.52799 (349/661)

Zygosity

Heterozygous

Amino Acid Change (HGVSp)

NP_071407.4:p.Ser496Asn

User Classification

BenignACMG Classification

BenignACMG Labels

BA1(gnomAD),BS1(gnomAD),BS3(ClinVar),BP1(ClinVar),BP4(SIFT)

Inheritance Pattern

Recessive

Variant Function

missense_variant

Allele frequency in gnomAD - whole
population

0.2736

Allele frequency in gnomAD - East Asian

0.29731000 Genomes Minor Allele

A

1000 Genomes Minor Allele Frequency

0.2524

SIFT Prediction

tolerated

dbSNP ID

rs10999947

ClinVar ID

45875

ClinVar Pathogenicity

BenignHGMD-

GEM-J WGA Allele Frequency

0.201

Report Inclusion

None

Variant (HGVSc)

NM_022124.6:c.2316T>C

Uncontrolled when printed

21/79

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posi_conGene Symbol

CDH23

Variant Type

SNV

Location

10:71695444-71695444

Exon Numbers

22/70

Ref

T

Alt

C

Frequency (Read)

0.42779 (391/914)

Zygosity

Heterozygous

Amino Acid Change (HGVSp)

NP_071407.4:p.Asn772=

User Classification

BenignACMG Classification

BenignACMG Labels

BA1(gnomAD),BS1(gnomAD),BS3(ClinVar),BP7(VEP,dbscSNV,GERP)

Inheritance Pattern

Recessive

Variant Functionsynonymous_variant

Allele frequency in gnomAD - whole
population

0.6284

Allele frequency in gnomAD - East Asian

0.50341000 Genomes Minor Allele

C

1000 Genomes Minor Allele Frequency

0.5545

SIFT Prediction-

dbSNP ID

rs3752752

ClinVar ID

45893

ClinVar Pathogenicity

BenignHGMD-

GEM-J WGA Allele Frequency

0.456

Report Inclusion

None

Variant (HGVSc)

NM_022124.6:c.2388T>C

Gene Symbol

CDH23

Variant Type

SNV

Location

10:71695516-71695516

Exon Numbers

22/70

Ref

T

Alt

C

Frequency (Read)

0.41463 (340/820)

Zygosity

Heterozygous

Amino Acid Change (HGVSp)

NP_071407.4:p.Asp796=

User Classification

BenignACMG Classification

BenignACMG Labels

BA1(gnomAD),BS1(gnomAD),BS3(ClinVar),BP7(VEP,dbscSNV,GERP)

Inheritance Pattern

Recessive

Variant Functionsynonymous_variant

Allele frequency in gnomAD - whole
population

0.6282

Allele frequency in gnomAD - East Asian

0.50081000 Genomes Minor Allele

C

1000 Genomes Minor Allele Frequency

0.5539SIFT Prediction-

dbSNP ID

rs3752751

ClinVar ID

45896

ClinVar Pathogenicity

BenignHGMD-

GEM-J WGA Allele Frequency

0.452

Report Inclusion

None

Variant (HGVSc)

NM_022124.6:c.3009T>C

Gene Symbol

CDH23

Variant Type

SNV

Location

10:71706952-71706952

Exon Numbers

26/70

Ref

T

Alt

C

Frequency (Read)

0.48642 (394/810)

Zygosity

Heterozygous

Amino Acid Change (HGVSp)

NP_071407.4:p.Ser1003=

User Classification

BenignACMG Classification

BenignACMG Labels

BA1(gnomAD),BS1(gnomAD),BS3(ClinVar),BP7(VEP,dbscSNV,GERP)

Inheritance Pattern

Recessive

Variant Functionsynonymous_variant

Allele frequency in gnomAD - whole
population

0.1034

Allele frequency in gnomAD - East Asian

0.25441000 Genomes Minor Allele

C

Uncontrolled when printed

22/79

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60

posi_con1000 Genomes Minor Allele Frequency

0.2075

SIFT Prediction-

dbSNP ID

rs10823829

ClinVar ID

44111

ClinVar Pathogenicity

BenignHGMD-

GEM-J WGA Allele Frequency

0.314

Report Inclusion

None

Variant (HGVSc)

NM_022124.6:c.3369+298C>G

Gene Symbol

CDH23

Variant Type

SNV

Location

10:71713111-71713111

Exon Numbers

Intronic

Ref

C

Alt

G

Frequency (Read)

0.43876 (326/743)

Zygosity

Heterozygous

Amino Acid Change (HGVSp)-

User Classification

BenignACMG Classification

BenignACMG Labels

BA1(gnomAD),BS1(gnomAD),BP6(ClinVar)

Inheritance Pattern

Recessive

Variant Function

intron_variant

Allele frequency in gnomAD - whole
population

0.317

Allele frequency in gnomAD - East Asian

0.44751000 Genomes Minor Allele

G

1000 Genomes Minor Allele Frequency

0.4499SIFT Prediction-

dbSNP ID

rs2394838

ClinVar ID

680503

ClinVar Pathogenicity

BenignHGMD-

GEM-J WGA Allele Frequency

0.412

Report Inclusion

None

Variant (HGVSc)

NM_022124.6:c.3369+312C>T

Gene Symbol

CDH23

Variant Type

SNV

Location

10:71713125-71713125

Exon Numbers

Intronic

Ref

C

Alt

T

Frequency (Read)

0.45308 (338/746)

Zygosity

Heterozygous

Amino Acid Change (HGVSp)-

User Classification

BenignACMG Classification

BenignACMG Labels

BA1(gnomAD),BS1(gnomAD),BP6(ClinVar)

Inheritance Pattern

Recessive

Variant Function

intron_variant

Allele frequency in gnomAD - whole
population

0.3148Allele frequency in gnomAD - East Asian

0.44591000 Genomes Minor Allele

T1000 Genomes Minor Allele Frequency

0.4413

SIFT Prediction-

dbSNP ID

rs2166631

ClinVar ID

680504

ClinVar Pathogenicity

BenignHGMD-

GEM-J WGA Allele Frequency

0.413

Report Inclusion

None

Variant (HGVSc)

NM_022124.6:c.4051A>G

Gene Symbol

CDH23

Variant Type

SNV

Location

10:71732322-71732322

Exon Numbers

32/70

Ref

A

Alt

G

Frequency (Read)

0.4908 (507/1033)

Zygosity

Heterozygous

Amino Acid Change (HGVSp)

NP_071407.4:p.Asn1351Asp

Uncontrolled when printed

23/79

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posi_con

User Classification

BenignACMG Classification

BenignACMG Labels

BA1(gnomAD),BS1(gnomAD),BS3(ClinVar),BP1(ClinVar),BP4(SIFT)

Inheritance Pattern

Recessive

Variant Function

missense_variant

Allele frequency in gnomAD - whole
population

0.8069Allele frequency in gnomAD - East Asian

0.84651000 Genomes Minor Allele

G

1000 Genomes Minor Allele Frequency

0.7821

SIFT Prediction

tolerated

dbSNP ID

rs1227065

ClinVar ID

45937

ClinVar Pathogenicity

BenignHGMD-

GEM-J WGA Allele Frequency

0.817

Report Inclusion

None

Variant (HGVSc)

NM_022124.6:c.4310G>A

Gene Symbol

CDH23

Variant Type

SNV

Location

10:71738598-71738598

Exon Numbers

35/70

Ref

G

Alt

A

Frequency (Read)

0.46705 (404/865)

Zygosity

Heterozygous

Amino Acid Change (HGVSp)

NP_071407.4:p.Arg1437Gln

User Classification

BenignACMG Classification

BenignACMG Labels

PM5(HGMD,ClinVar),BS1(gnomAD),BS3(ClinVar),BP1(ClinVar),BP4(SIFT)

Inheritance Pattern

Recessive

Variant Function

missense_variant

Allele frequency in gnomAD - whole
population

0.03607

Allele frequency in gnomAD - East Asian

0.08751000 Genomes Minor Allele

A

1000 Genomes Minor Allele Frequency

0.0521

SIFT Prediction

tolerated

dbSNP ID

rs56181447

ClinVar ID

45944

ClinVar Pathogenicity

Benign/Likely_benign

HGMD

-

GEM-J WGA Allele Frequency

0.118

Report Inclusion

None

Variant (HGVSc)

NM_022124.6:c.4723G>A

Gene Symbol

CDH23

Variant Type

SNV

Location

10:71741799-71741799

Exon Numbers

38/70

Ref

G

Alt

A

Frequency (Read)

0.46214 (415/898)

Zygosity

Heterozygous

Amino Acid Change (HGVSp)

NP_071407.4:p.Ala1575Thr

User Classification

BenignACMG Classification

BenignACMG Labels

BA1(gnomAD),BS1(gnomAD),BS3(ClinVar),BP1(ClinVar),BP4(SIFT)

Inheritance Pattern

Recessive

Variant Function

missense_variant

Allele frequency in gnomAD - whole
population

0.7742

Allele frequency in gnomAD - East Asian

0.83231000 Genomes Minor Allele

A

1000 Genomes Minor Allele Frequency

0.7288SIFT Prediction

tolerated

dbSNP ID

rs1227051

ClinVar ID

45955

ClinVar Pathogenicity

BenignHGMD-

GEM-J WGA Allele Frequency

0.815

Report Inclusion

None

Variant (HGVSc)

NM_022124.6:c.5023G>A

Uncontrolled when printed

24/79

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posi_conGene Symbol

CDH23

Variant Type

SNV

Location

10:71777857-71777857

Exon Numbers

39/70

Ref

G

Alt

A

Frequency (Read)

0.50715 (461/909)

Zygosity

Heterozygous

Amino Acid Change (HGVSp)

NP_071407.4:p.Val1675Ile

User Classification

BenignACMG Classification

BenignACMG Labels

BA1(gnomAD),BS1(gnomAD),BS3(ClinVar),BP1(ClinVar),BP4(SIFT)

Inheritance Pattern

Recessive

Variant Function

missense_variant

Allele frequency in gnomAD - whole
population

0.1793

Allele frequency in gnomAD - East Asian

0.16041000 Genomes Minor Allele

A

1000 Genomes Minor Allele Frequency

0.1322SIFT Prediction

tolerated

dbSNP ID

rs17712523

ClinVar ID

45960

ClinVar Pathogenicity

BenignHGMD-

GEM-J WGA Allele Frequency

0.142

Report Inclusion

None

Variant (HGVSc)

NM_022124.6:c.5100C>T

Gene Symbol

CDH23

Variant Type

SNV

Location

10:71778221-71778221

Exon Numbers

40/70

Ref

C

Alt

T

Frequency (Read)

0.50911 (391/768)

Zygosity

Heterozygous

Amino Acid Change (HGVSp)

NP_071407.4:p.Tyr1700=

User Classification

BenignACMG Classification

BenignACMG Labels

BA1(gnomAD),BS1(gnomAD),BS3(ClinVar),BP7(VEP,dbscSNV,GERP)

Inheritance Pattern

Recessive

Variant Functionsynonymous_variant

Allele frequency in gnomAD - whole
population

0.1868Allele frequency in gnomAD - East Asian

0.18641000 Genomes Minor Allele

T1000 Genomes Minor Allele Frequency

0.1793

SIFT Prediction-

dbSNP ID

rs10762480

ClinVar ID

45965

ClinVar Pathogenicity

BenignHGMD-

GEM-J WGA Allele Frequency

0.239

Report Inclusion

None

Variant (HGVSc)

NM_022124.6:c.5411G>A

Gene Symbol

CDH23

Variant Type

SNV

Location

10:71784329-71784329

Exon Numbers

42/70

Ref

G

Alt

A

Frequency (Read)

0.52174 (396/759)

Zygosity

Heterozygous

Amino Acid Change (HGVSp)

NP_071407.4:p.Arg1804Gln

User Classification

BenignACMG Classification

BenignACMG Labels

BA1(gnomAD),BS1(gnomAD),BS3(ClinVar),BP1(ClinVar),BP4(SIFT)

Inheritance Pattern

Recessive

Variant Function

missense_variant

Allele frequency in gnomAD - whole
population

0.155

Allele frequency in gnomAD - East Asian

0.23651000 Genomes Minor Allele

A

Uncontrolled when printed

25/79

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posi_con1000 Genomes Minor Allele Frequency

0.139

SIFT Prediction

tolerated

dbSNP ID

rs3802711

ClinVar ID

45978

ClinVar Pathogenicity

BenignHGMD-

GEM-J WGA Allele Frequency

0.294

Report Inclusion

None

Variant (HGVSc)

NM_022124.6:c.5996C>G

Gene Symbol

CDH23

Variant Type

SNV

Location

10:71790360-71790360

Exon Numbers

46/70

Ref

C

Alt

G

Frequency (Read)

0.49035 (432/881)

Zygosity

Heterozygous

Amino Acid Change (HGVSp)

NP_071407.4:p.Thr1999Ser

User Classification

BenignACMG Classification

BenignACMG Labels

BA1(gnomAD),BS1(gnomAD),BS3(ClinVar),BP1(ClinVar),BP4(SIFT)

Inheritance Pattern

Recessive

Variant Function

missense_variant

Allele frequency in gnomAD - whole
population

0.4229Allele frequency in gnomAD - East Asian

0.16481000 Genomes Minor Allele

G

1000 Genomes Minor Allele Frequency

0.3452SIFT Prediction

tolerated

dbSNP ID

rs11592462

ClinVar ID

45997

ClinVar Pathogenicity

BenignHGMD-

GEM-J WGA Allele Frequency

0.133

Report Inclusion

None

Variant (HGVSc)

NM_022124.6:c.6130G>A

Gene Symbol

CDH23

Variant Type

SNV

Location

10:71791212-71791212

Exon Numbers

47/70

Ref

G

Alt

A

Frequency (Read)

0.47732 (463/970)

Zygosity

Heterozygous

Amino Acid Change (HGVSp)

NP_071407.4:p.Glu2044Lys

User Classification

BenignACMG Classification

BenignACMG Labels

BA1(gnomAD),BS1(gnomAD),BS3(ClinVar),BP1(ClinVar),BP4(SIFT)

Inheritance Pattern

Recessive

Variant Function

missense_variant

Allele frequency in gnomAD - whole
population

0.3093

Allele frequency in gnomAD - East Asian

0.52871000 Genomes Minor Allele

A

1000 Genomes Minor Allele Frequency

0.3327

SIFT Prediction

tolerated

dbSNP ID

rs10466026

ClinVar ID

46002

ClinVar Pathogenicity

BenignHGMD-

GEM-J WGA Allele Frequency

0.605

Report Inclusion

None

Variant (HGVSc)

NM_022124.6:c.7073G>A

Gene Symbol

CDH23

Variant Type

SNV

Location

10:71799129-71799129

Exon Numbers

51/70

Ref

G

Alt

A

Frequency (Read)

0.46009 (317/689)

Zygosity

Heterozygous

Amino Acid Change (HGVSp)

NP_071407.4:p.Arg2358Gln

Uncontrolled when printed

26/79

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70

71

posi_con

User Classification

BenignACMG Classification

BenignACMG Labels

BA1(gnomAD),BS1(gnomAD),BS3(ClinVar),BP1(ClinVar),BP4(SIFT)

Inheritance Pattern

Recessive

Variant Function

missense_variant

Allele frequency in gnomAD - whole
population

0.3149Allele frequency in gnomAD - East Asian

0.52991000 Genomes Minor Allele

A

1000 Genomes Minor Allele Frequency

0.3413

SIFT Prediction

tolerated

dbSNP ID

rs4747194

ClinVar ID

46026

ClinVar Pathogenicity

BenignHGMD-

GEM-J WGA Allele Frequency

0.605

Report Inclusion

None

Variant (HGVSc)

NM_022124.6:c.7139C>T

Gene Symbol

CDH23

Variant Type

SNV

Location

10:71799195-71799195

Exon Numbers

51/70

Ref

C

Alt

T

Frequency (Read)

0.48904 (424/867)

Zygosity

Heterozygous

Amino Acid Change (HGVSp)

NP_071407.4:p.Pro2380Leu

User Classification

BenignACMG Classification

BenignACMG Labels

PP3(SIFT),BA1(gnomAD),BS1(gnomAD),BS3(ClinVar),BP1(ClinVar)

Inheritance Pattern

Recessive

Variant Function

missense_variant

Allele frequency in gnomAD - whole
population

0.3081Allele frequency in gnomAD - East Asian

0.52961000 Genomes Minor Allele

T1000 Genomes Minor Allele Frequency

0.3283

SIFT Predictiondeleterious

dbSNP ID

rs4747195

ClinVar ID

46028

ClinVar Pathogenicity

BenignHGMD-

GEM-J WGA Allele Frequency

0.605

Report Inclusion

None

Variant (HGVSc)

NM_022124.6:c.7572G>A

Gene Symbol

CDH23

Variant Type

SNV

Location

10:71802987-71802987

Exon Numbers

54/70

Ref

G

Alt

A

Frequency (Read)

0.44264 (382/863)

Zygosity

Heterozygous

Amino Acid Change (HGVSp)

NP_071407.4:p.Ala2524=

User Classification

BenignACMG Classification

BenignACMG Labels

BA1(gnomAD),BS1(gnomAD),BS3(ClinVar),BP7(VEP,dbscSNV,GERP)

Inheritance Pattern

Recessive

Variant Functionsynonymous_variant

Allele frequency in gnomAD - whole
population

0.3106

Allele frequency in gnomAD - East Asian

0.52681000 Genomes Minor Allele

A

1000 Genomes Minor Allele Frequency

0.3285

SIFT Prediction-

dbSNP ID

rs10823849

ClinVar ID

46034

ClinVar Pathogenicity

BenignHGMD-

GEM-J WGA Allele Frequency

0.606

Report Inclusion

None

Variant (HGVSc)

NM_022124.6:c.9077+8G>A

Uncontrolled when printed

27/79

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posi_conGene Symbol

CDH23

Variant Type

SNV

Location

10:71810577-71810577

Exon Numbers

Intronic

Ref

G

Alt

A

Frequency (Read)

0.5308 (405/763)

Zygosity

Heterozygous

Amino Acid Change (HGVSp)-

User Classification

BenignACMG Classification

BenignACMG Labels

BA1(gnomAD),BS1(gnomAD),BS3(ClinVar),BP4(dbscSNV)

Inheritance Pattern

Recessive

Variant Function

splice_region_variant,intron_variant

Allele frequency in gnomAD - whole
population

0.1685Allele frequency in gnomAD - East Asian

0.23631000 Genomes Minor Allele

A

1000 Genomes Minor Allele Frequency

0.1486

SIFT Prediction-

dbSNP ID

rs11818398

ClinVar ID

46068

ClinVar Pathogenicity

BenignHGMD-

GEM-J WGA Allele Frequency

0.302

Report Inclusion

None

Variant (HGVSc)

NM_033100.4:c.477A>G

Gene Symbol

CDHR1

Variant Type

SNV

Location

10:84200639-84200639

Exon Numbers

6/17

Ref

A

Alt

G

Frequency (Read)

0.47152 (356/755)

Zygosity

Heterozygous

Amino Acid Change (HGVSp)

NP_149091.1:p.Ala159=

User Classification

BenignACMG Classification

BenignACMG Labels

BA1(gnomAD),BS1(gnomAD),BS3(ClinVar),BP7(VEP,dbscSNV,GERP)

Inheritance Pattern

Recessive

Variant Functionsynonymous_variant

Allele frequency in gnomAD - whole
population

0.4739Allele frequency in gnomAD - East Asian

0.37971000 Genomes Minor Allele

G

1000 Genomes Minor Allele Frequency

0.516

SIFT Prediction-

dbSNP ID

rs4933975

ClinVar ID

262215

ClinVar Pathogenicity

BenignHGMD-

GEM-J WGA Allele Frequency

0.305

Report Inclusion

None

Variant (HGVSc)

NM_033100.4:c.2439T>C

Gene Symbol

CDHR1

Variant Type

SNV

Location

10:84214480-84214480

Exon Numbers

17/17

Ref

T

Alt

C

Frequency (Read)

0.49097 (408/831)

Zygosity

Heterozygous

Amino Acid Change (HGVSp)

NP_149091.1:p.Thr813=

User Classification

BenignACMG Classification

BenignACMG Labels

BA1(gnomAD),BS1(gnomAD),BS3(ClinVar),BP7(VEP,dbscSNV,GERP)

Inheritance Pattern

Recessive

Variant Functionsynonymous_variant

Allele frequency in gnomAD - whole
population

0.5321Allele frequency in gnomAD - East Asian

0.39271000 Genomes Minor Allele

C

Uncontrolled when printed

28/79

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75

76

posi_con1000 Genomes Minor Allele Frequency

0.5737

SIFT Prediction-

dbSNP ID

rs3814213

ClinVar ID

194794

ClinVar Pathogenicity

BenignHGMD-

GEM-J WGA Allele Frequency

0.311

Report Inclusion

None

Variant (HGVSc)

NM_033100.4:c.*4A>G

Gene Symbol

CDHR1

Variant Type

SNV

Location

10:84214625-84214625

Exon Numbers

17/17

Ref

A

Alt

G

Frequency (Read)

0.53737 (266/495)

Zygosity

Heterozygous

Amino Acid Change (HGVSp)-

User Classification

BenignACMG Classification

BenignACMG Labels

BA1(gnomAD),BS1(gnomAD),BS3(ClinVar)

Inheritance Pattern

Recessive

Variant Function

3_prime_UTR_variant

Allele frequency in gnomAD - whole
population

0.5861Allele frequency in gnomAD - East Asian

0.39341000 Genomes Minor Allele

G

1000 Genomes Minor Allele Frequency

0.6274

SIFT Prediction-

dbSNP ID

rs3814212

ClinVar ID

194795

ClinVar Pathogenicity

BenignHGMD-

GEM-J WGA Allele Frequency

0.311

Report Inclusion

None

Variant (HGVSc)-

Gene Symbol

CDHR1

Variant Type

SNV

Location

10:84219183-84219183

Exon Numbers

Intronic

Ref

G

Alt

A

Frequency (Read)

0.48636 (321/660)

Zygosity

Heterozygous

Amino Acid Change (HGVSp)-

User Classification

BenignACMG Classification

BenignACMG Labels

BA1(gnomAD),BS1(gnomAD),BP6(ClinVar)

Inheritance Pattern

Recessive

Variant Function

downstream_gene_variant

Allele frequency in gnomAD - whole
population

0.491

Allele frequency in gnomAD - East Asian

0.39351000 Genomes Minor Allele

A

1000 Genomes Minor Allele Frequency

0.5541

SIFT Prediction-

dbSNP ID

rs4244947

ClinVar ID

1192715

ClinVar Pathogenicity

BenignHGMD-

GEM-J WGA Allele Frequency

0.311

Report Inclusion

None

Variant (HGVSc)

NM_025114.4:c.3574-9delGene Symbol

CEP290

Variant Type

Deletion

Location

12:88089495-88089496

Exon Numbers

Intronic

Ref

TA

Alt

T

Frequency (Read)

0.98387 (244/248)

Zygosity

Homozygous

Amino Acid Change (HGVSp)-

Uncontrolled when printed

29/79

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posi_con

User Classification

BenignACMG Classification

BenignACMG Labels

BA1(gnomAD),BS1(gnomAD),BS3(ClinVar)

Inheritance Pattern

Recessive

Variant Function

splice_polypyrimidine_tract_variant,intron_variant

Allele frequency in gnomAD - whole
population

0.9308Allele frequency in gnomAD - East Asian

0.99041000 Genomes Minor Allele-

1000 Genomes Minor Allele Frequency

0.8736

SIFT Prediction-

dbSNP ID

rs10717563

ClinVar ID

96170

ClinVar Pathogenicity

BenignHGMD-

GEM-J WGA Allele Frequency

0.997

Report Inclusion

None

Variant (HGVSc)

NM_025114.4:c.2268A>G

Gene Symbol

CEP290

Variant Type

SNV

Location

12:88111301-88111301

Exon Numbers

22/54

Ref

T

Alt

C

Frequency (Read)

1.0 (349/349)

Zygosity

Homozygous

Amino Acid Change (HGVSp)

NP_079390.3:p.Ser756=

User Classification

BenignACMG Classification

BenignACMG Labels

BA1(gnomAD),BS1(gnomAD),BS3(ClinVar),BP7(VEP,dbscSNV,GERP)

Inheritance Pattern

Recessive

Variant Functionsynonymous_variant

Allele frequency in gnomAD - whole
population

0.8938Allele frequency in gnomAD - East Asian

0.97551000 Genomes Minor Allele

C

1000 Genomes Minor Allele Frequency

0.7646

SIFT Prediction-

dbSNP ID

rs2468255

ClinVar ID

126249ClinVar Pathogenicity

BenignHGMD-

GEM-J WGA Allele Frequency

0.937

Report Inclusion

None

Variant (HGVSc)

NM_025114.4:c.2055T>C

Gene Symbol

CEP290

Variant Type

SNV

Location

12:88111856-88111856

Exon Numbers

21/54

Ref

A

Alt

G

Frequency (Read)

0.51323 (97/189)

Zygosity

Heterozygous

Amino Acid Change (HGVSp)

NP_079390.3:p.Ala685=

User Classification

BenignACMG Classification

BenignACMG Labels

BA1(gnomAD),BS1(gnomAD),BS3(ClinVar),BP7(VEP,dbscSNV,GERP)

Inheritance Pattern

Recessive

Variant Function

splice_region_variant,synonymous_variant

Allele frequency in gnomAD - whole
population

0.1382

Allele frequency in gnomAD - East Asian

8.134E-5

1000 Genomes Minor Allele

G

1000 Genomes Minor Allele Frequency

0.0689SIFT Prediction-

dbSNP ID

rs45465996

ClinVar ID

96168

ClinVar Pathogenicity

BenignHGMD-

GEM-J WGA Allele Frequency-

Report Inclusion

None

Variant (HGVSc)

NM_001030311.3:c.1584C>T

Uncontrolled when printed

30/79

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81

posi_conGene Symbol

CERKL

Variant Type

SNV

Location

2:181539124-181539124

Exon Numbers

13/14

Ref

G

Alt

A

Frequency (Read)

1.0 (438/438)

Zygosity

Homozygous

Amino Acid Change (HGVSp)

NP_001025482.1:p.Asp528=

User Classification

BenignACMG Classification

BenignACMG Labels

BA1(gnomAD),BS1(gnomAD),BS3(ClinVar),BP7(VEP,dbscSNV,GERP)

Inheritance Pattern

Recessive

Variant Functionsynonymous_variant

Allele frequency in gnomAD - whole
population

0.9979Allele frequency in gnomAD - East Asian

1.01000 Genomes Minor Allele

A

1000 Genomes Minor Allele Frequency

0.9912SIFT Prediction-

dbSNP ID

rs10180793

ClinVar ID

166844

ClinVar Pathogenicity

BenignHGMD-

GEM-J WGA Allele Frequency

1.0

Report Inclusion

None

Variant (HGVSc)

NM_001030311.3:c.156C>T

Gene Symbol

CERKL

Variant Type

SNV

Location

2:181656851-181656851

Exon Numbers

1/14

Ref

G

Alt

A

Frequency (Read)

0.47279 (443/937)

Zygosity

Heterozygous

Amino Acid Change (HGVSp)

NP_001025482.1:p.Phe52=

User Classification

BenignACMG Classification

BenignACMG Labels

BA1(gnomAD),BS1(gnomAD),BS3(ClinVar),BP7(VEP,dbscSNV,GERP)

Inheritance Pattern

Recessive

Variant Functionsynonymous_variant

Allele frequency in gnomAD - whole
population

0.5276

Allele frequency in gnomAD - East Asian

0.71091000 Genomes Minor Allele

A

1000 Genomes Minor Allele Frequency

0.5074

SIFT Prediction-

dbSNP ID

rs1473295

ClinVar ID

166849ClinVar Pathogenicity

BenignHGMD-

GEM-J WGA Allele Frequency

0.742

Report Inclusion

None

Variant (HGVSc)

NM_004928.3:c.449C>T

Gene Symbol

CFAP410

Variant Type

SNV

Location

21:44331939-44331939

Exon Numbers

5/7

Ref

G

Alt

A

Frequency (Read)

0.48362 (443/916)

Zygosity

Heterozygous

Amino Acid Change (HGVSp)

NP_004919.1:p.Thr150Ile

User Classification

BenignACMG Classification

BenignACMG Labels

PP3(BLOSUM),BS1(gnomAD),BS3(ClinVar),BP1(ClinVar),BP4(SIFT)

Inheritance Pattern

Recessive

Variant Function

missense_variant

Allele frequency in gnomAD - whole
population

0.02902

Allele frequency in gnomAD - East Asian

0.05725

1000 Genomes Minor Allele

A

Uncontrolled when printed

31/79

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84

posi_con1000 Genomes Minor Allele Frequency

0.0373

SIFT Prediction

tolerated

dbSNP ID

rs2277809

ClinVar ID

259587

ClinVar Pathogenicity

BenignHGMD-

GEM-J WGA Allele Frequency

0.068

Report Inclusion

None

Variant (HGVSc)

NM_004928.3:c.33G>A

Gene Symbol

CFAP410

Variant Type

SNV

Location

21:44339162-44339162

Exon Numbers

1/7

Ref

C

Alt

T

Frequency (Read)

0.44395 (301/678)

Zygosity

Heterozygous

Amino Acid Change (HGVSp)

NP_004919.1:p.Arg11=

User Classification

BenignACMG Classification

BenignACMG Labels

BA1(gnomAD),BS1(gnomAD),BS3(ClinVar),BP7(VEP,dbscSNV,GERP)

Inheritance Pattern

Recessive

Variant Functionsynonymous_variant

Allele frequency in gnomAD - whole
population

0.2403

Allele frequency in gnomAD - East Asian

0.12991000 Genomes Minor Allele

T1000 Genomes Minor Allele Frequency

0.3261

SIFT Prediction-

dbSNP ID

rs11870

ClinVar ID

259586

ClinVar Pathogenicity

BenignHGMD-

GEM-J WGA Allele Frequency

0.166

Report Inclusion

None

Variant (HGVSc)

NM_000087.5:c.-15+10300C>T

Gene Symbol

CNGA1

Variant Type

SNV

Location

4:47971093-47971093

Exon Numbers

Intronic

Ref

G

Alt

A

Frequency (Read)

1.0 (240/240)

Zygosity

Homozygous

Amino Acid Change (HGVSp)-

User Classification

BenignACMG Classification

BenignACMG Labels

BA1(gnomAD),BS1(gnomAD),BP6(ClinVar)

Inheritance Pattern

Recessive

Variant Function

intron_variant

Allele frequency in gnomAD - whole
population

0.5657

Allele frequency in gnomAD - East Asian

0.29941000 Genomes Minor Allele

A

1000 Genomes Minor Allele Frequency

0.4593

SIFT Prediction-

dbSNP ID

rs7693648

ClinVar ID

1217361

ClinVar Pathogenicity

BenignHGMD-

GEM-J WGA Allele Frequency

0.266

Report Inclusion

None

Variant (HGVSc)

NM_001298.3:c.72T>C

Gene Symbol

CNGA3

Variant Type

SNV

Location

2:98370047-98370047

Exon Numbers

2/8

Ref

T

Alt

C

Frequency (Read)

0.48667 (365/750)

Zygosity

Heterozygous

Amino Acid Change (HGVSp)

NP_001289.1:p.Asp24=

Uncontrolled when printed

32/79

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posi_con

User Classification

BenignACMG Classification

BenignACMG Labels

BA1(gnomAD),BS1(gnomAD),BS3(ClinVar),BP7(VEP,dbscSNV,GERP)

Inheritance Pattern

Recessive

Variant Functionsynonymous_variant

Allele frequency in gnomAD - whole
population

0.1327

Allele frequency in gnomAD - East Asian

0.006253

1000 Genomes Minor Allele

C

1000 Genomes Minor Allele Frequency

0.0899SIFT Prediction-

dbSNP ID

rs6727412

ClinVar ID

257964

ClinVar Pathogenicity

BenignHGMD-

GEM-J WGA Allele Frequency

0.002251

Report Inclusion

None

Variant (HGVSc)

NM_001297.5:c.3462+7T>C

Gene Symbol

CNGB1

Variant Type

SNV

Location

16:57887848-57887848

Exon Numbers

Intronic

Ref

A

Alt

G

Frequency (Read)

0.48758 (314/644)

Zygosity

Heterozygous

Amino Acid Change (HGVSp)-

User Classification

BenignACMG Classification

BenignACMG Labels

BA1(gnomAD),BS1(gnomAD),BS3(ClinVar),BP4(dbscSNV)

Inheritance Pattern

Recessive

Variant Function

splice_region_variant,intron_variant

Allele frequency in gnomAD - whole
population

0.3071Allele frequency in gnomAD - East Asian

0.34221000 Genomes Minor Allele

G

1000 Genomes Minor Allele Frequency

0.3702SIFT Prediction-

dbSNP ID

rs11076207

ClinVar ID

320059ClinVar Pathogenicity

BenignHGMD-

GEM-J WGA Allele Frequency

0.234

Report Inclusion

None

Variant (HGVSc)

NM_001297.5:c.2664C>GGene Symbol

CNGB1

Variant Type

SNV

Location

16:57903952-57903952

Exon Numbers

27/33

Ref

G

Alt

C

Frequency (Read)

0.50357 (353/701)

Zygosity

Heterozygous

Amino Acid Change (HGVSp)

NP_001288.3:p.Ala888=

User Classification

BenignACMG Classification

BenignACMG Labels

BA1(gnomAD),BS1(gnomAD),BS3(ClinVar),BP7(VEP,dbscSNV,GERP)

Inheritance Pattern

Recessive

Variant Functionsynonymous_variant

Allele frequency in gnomAD - whole
population

0.7653

Allele frequency in gnomAD - East Asian

0.9181000 Genomes Minor Allele

C

1000 Genomes Minor Allele Frequency

0.7049SIFT Prediction-

dbSNP ID

rs413562

ClinVar ID

166894

ClinVar Pathogenicity

BenignHGMD-

GEM-J WGA Allele Frequency

0.952

Report Inclusion

None

Variant (HGVSc)

NM_001297.5:c.2635-10C>T

Uncontrolled when printed

33/79

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89

posi_conGene Symbol

CNGB1

Variant Type

SNV

Location

16:57903991-57903991

Exon Numbers

Intronic

Ref

G

Alt

A

Frequency (Read)

0.4912 (279/568)

Zygosity

Heterozygous

Amino Acid Change (HGVSp)-

User Classification

BenignACMG Classification

BenignACMG Labels

BA1(gnomAD),BS1(gnomAD),BS3(ClinVar)

Inheritance Pattern

Recessive

Variant Function

splice_polypyrimidine_tract_variant,intron_variant

Allele frequency in gnomAD - whole
population

0.812

Allele frequency in gnomAD - East Asian

0.65651000 Genomes Minor Allele

A

1000 Genomes Minor Allele Frequency

0.7484

SIFT Prediction-

dbSNP ID

rs437920

ClinVar ID

166895

ClinVar Pathogenicity

BenignHGMD-

GEM-J WGA Allele Frequency

0.636

Report Inclusion

None

Variant (HGVSc)

NM_001297.5:c.327C>T

Gene Symbol

CNGB1

Variant Type

SNV

Location

16:57963028-57963028

Exon Numbers

5/33

Ref

G

Alt

A

Frequency (Read)

0.49537 (428/864)

Zygosity

Heterozygous

Amino Acid Change (HGVSp)

NP_001288.3:p.Gly109=

User Classification

BenignACMG Classification

BenignACMG Labels

BA1(gnomAD),BS1(gnomAD),BS3(ClinVar),BP7(VEP,dbscSNV,GERP)

Inheritance Pattern

Recessive

Variant Functionsynonymous_variant

Allele frequency in gnomAD - whole
population

0.4306

Allele frequency in gnomAD - East Asian

0.33091000 Genomes Minor Allele

A

1000 Genomes Minor Allele Frequency

0.3141

SIFT Prediction-

dbSNP ID

rs17821448

ClinVar ID

320109ClinVar Pathogenicity

BenignHGMD-

GEM-J WGA Allele Frequency

0.345

Report Inclusion

None

Variant (HGVSc)

NM_001297.5:c.299G>A

Gene Symbol

CNGB1

Variant Type

SNV

Location

16:57963056-57963056

Exon Numbers

5/33

Ref

C

Alt

T

Frequency (Read)

0.99875 (798/799)

Zygosity

Homozygous

Amino Acid Change (HGVSp)

NP_001288.3:p.Arg100His

User Classification

BenignACMG Classification

BenignACMG Labels

PP3(SIFT),BA1(gnomAD),BS1(gnomAD),BS3(ClinVar),BP1(ClinVar),BP6(Benign Variants from PMID:31213501)

Inheritance Pattern

Recessive

Variant Function

missense_variant

Allele frequency in gnomAD - whole
population

0.7822

Allele frequency in gnomAD - East Asian

0.8441000 Genomes Minor Allele

T

Uncontrolled when printed

34/79

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92

posi_con1000 Genomes Minor Allele Frequency

0.752

SIFT Predictiondeleterious_low_confidence

dbSNP ID

rs13336595

ClinVar ID

320110

ClinVar Pathogenicity

BenignHGMD-

GEM-J WGA Allele Frequency

0.837

Report Inclusion

None

Variant (HGVSc)

NM_019098.5:c.892A>C

Gene Symbol

CNGB3

Variant Type

SNV

Location

8:86654023-86654023

Exon Numbers

7/18

Ref

T

Alt

G

Frequency (Read)

1.0 (314/314)

Zygosity

Homozygous

Amino Acid Change (HGVSp)

NP_061971.3:p.Thr298Pro

User Classification

BenignACMG Classification

BenignACMG Labels

PP3(BLOSUM),BA1(gnomAD),BS1(gnomAD),BS3(ClinVar),BP1(ClinVar),BP4(SIFT)

Inheritance Pattern

Recessive

Variant Function

missense_variant

Allele frequency in gnomAD - whole
population

0.6607

Allele frequency in gnomAD - East Asian

0.79591000 Genomes Minor Allele

G

1000 Genomes Minor Allele Frequency

0.6797

SIFT Prediction

tolerated

dbSNP ID

rs4961206

ClinVar ID

95929

ClinVar Pathogenicity

BenignHGMD-

GEM-J WGA Allele Frequency

0.798

Report Inclusion

None

Variant (HGVSc)

NM_019098.5:c.702T>GGene Symbol

CNGB3

Variant Type

SNV

Location

8:86667075-86667075

Exon Numbers

6/18

Ref

A

Alt

C

Frequency (Read)

0.99848 (656/657)

Zygosity

Homozygous

Amino Acid Change (HGVSp)

NP_061971.3:p.Cys234Trp

User Classification

BenignACMG Classification

BenignACMG Labels

PP3(BLOSUM),BA1(gnomAD),BS1(gnomAD),BS3(ClinVar),BP1(ClinVar),BP4(SIFT)

Inheritance Pattern

Recessive

Variant Function

missense_variant

Allele frequency in gnomAD - whole
population

0.8925Allele frequency in gnomAD - East Asian

0.99981000 Genomes Minor Allele

C

1000 Genomes Minor Allele Frequency

0.9575

SIFT Prediction

tolerated

dbSNP ID

rs6471482

ClinVar ID

261090

ClinVar Pathogenicity

BenignHGMD-

GEM-J WGA Allele Frequency

1.0

Report Inclusion

None

Variant (HGVSc)

NM_019098.5:c.80A>G

Gene Symbol

CNGB3

Variant Type

SNV

Location

8:86743548-86743548

Exon Numbers

1/18

Ref

T

Alt

C

Frequency (Read)

0.52196 (309/592)

Zygosity

Heterozygous

Amino Acid Change (HGVSp)

NP_061971.3:p.Asn27Ser

Uncontrolled when printed

35/79

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94

95

posi_con

User Classification

BenignACMG Classification

BenignACMG Labels

BS1(gnomAD),BS3(ClinVar),BP1(ClinVar),BP4(SIFT)

Inheritance Pattern

Recessive

Variant Function

missense_variant

Allele frequency in gnomAD - whole
population

0.01846

Allele frequency in gnomAD - East Asian

5.437E-5

1000 Genomes Minor Allele

C

1000 Genomes Minor Allele Frequency

0.0066

SIFT Prediction

tolerated

dbSNP ID

rs35807406

ClinVar ID

100588

ClinVar Pathogenicity

Benign/Likely_benign

HGMD

-

GEM-J WGA Allele Frequency-

Report Inclusion

None

Variant (HGVSc)

NM_201253.3:c.1410A>G

Gene Symbol

CRB1

Variant Type

SNV

Location

1:197421238-197421238

Exon Numbers

6/12

Ref

A

Alt

G

Frequency (Read)

1.0 (705/705)

Zygosity

Homozygous

Amino Acid Change (HGVSp)

NP_957705.1:p.Leu470=

User Classification

BenignACMG Classification

BenignACMG Labels

BA1(gnomAD),BS1(gnomAD),BS3(ClinVar),BP7(VEP,dbscSNV,GERP)

Inheritance Pattern

Recessive

Variant Functionsynonymous_variant

Allele frequency in gnomAD - whole
population

0.9818Allele frequency in gnomAD - East Asian

0.99981000 Genomes Minor Allele

G

1000 Genomes Minor Allele Frequency

0.9197

SIFT Prediction-

dbSNP ID

rs3902057

ClinVar ID

166956

ClinVar Pathogenicity

BenignHGMD-

GEM-J WGA Allele Frequency

1.0

Report Inclusion

None

Variant (HGVSc)

NM_207352.4:c.64C>GGene Symbol

CYP4V2

Variant Type

SNV

Location

4:186191887-186191887

Exon Numbers

1/11

Ref

C

Alt

G

Frequency (Read)

0.50496 (509/1008)

Zygosity

Heterozygous

Amino Acid Change (HGVSp)

NP_997235.3:p.Leu22Val

User Classification

BenignACMG Classification

BenignACMG Labels

PM5(HGMD),BA1(gnomAD),BS1(gnomAD),BS3(ClinVar),BP4(SIFT)

Inheritance Pattern

Recessive

Variant Function

missense_variant

Allele frequency in gnomAD - whole
population

0.4436

Allele frequency in gnomAD - East Asian

0.27211000 Genomes Minor Allele

G

1000 Genomes Minor Allele Frequency

0.4097

SIFT Prediction

tolerated

dbSNP ID

rs1055138

ClinVar ID

39267

ClinVar Pathogenicity

BenignHGMD-

GEM-J WGA Allele Frequency

0.285

Report Inclusion

None

Variant (HGVSc)

NM_207352.4:c.775C>A

Uncontrolled when printed

36/79

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posi_conGene Symbol

CYP4V2

Variant Type

SNV

Location

4:186199057-186199057

Exon Numbers

6/11

Ref

C

Alt

A

Frequency (Read)

1.0 (392/392)

Zygosity

Homozygous

Amino Acid Change (HGVSp)

NP_997235.3:p.Gln259Lys

User Classification

BenignACMG Classification

BenignACMG Labels

BA1(gnomAD),BS1(gnomAD),BS3(ClinVar),BP4(SIFT),BP6(Benign Variants from PMID:31213501)

Inheritance Pattern

Recessive

Variant Function

missense_variant

Allele frequency in gnomAD - whole
population

0.5734

Allele frequency in gnomAD - East Asian

0.39351000 Genomes Minor Allele

A

1000 Genomes Minor Allele Frequency

0.5593

SIFT Prediction

tolerated

dbSNP ID

rs13146272

ClinVar ID

263297

ClinVar Pathogenicity

BenignHGMD-

GEM-J WGA Allele Frequency

0.396

Report Inclusion

None

Variant (HGVSc)

NM_207352.4:c.802-7C>T

Gene Symbol

CYP4V2

Variant Type

SNV

Location

4:186201150-186201150

Exon Numbers

Intronic

Ref

C

Alt

T

Frequency (Read)

1.0 (413/413)

Zygosity

Homozygous

Amino Acid Change (HGVSp)-

User Classification

BenignACMG Classification

BenignACMG Labels

BA1(gnomAD),BS1(gnomAD),BS3(ClinVar),BP4(dbscSNV)

Inheritance Pattern

Recessive

Variant Function

splice_polypyrimidine_tract_variant,splice_region_variant,intron_variant

Allele frequency in gnomAD - whole
population

0.3338Allele frequency in gnomAD - East Asian

0.33341000 Genomes Minor Allele

T1000 Genomes Minor Allele Frequency

0.2923

SIFT Prediction-

dbSNP ID

rs3817184

ClinVar ID

166975

ClinVar Pathogenicity

BenignHGMD-

GEM-J WGA Allele Frequency

0.332

Report Inclusion

None

Variant (HGVSc)

NM_207352.4:c.810T>G

Gene Symbol

CYP4V2

Variant Type

SNV

Location

4:186201165-186201165

Exon Numbers

7/11

Ref

T

Alt

G

Frequency (Read)

0.99796 (490/491)

Zygosity

Homozygous

Amino Acid Change (HGVSp)

NP_997235.3:p.Ala270=

User Classification

BenignACMG Classification

BenignACMG Labels

BA1(gnomAD),BS1(gnomAD),BS3(ClinVar),BP7(VEP,dbscSNV,GERP)

Inheritance Pattern

Recessive

Variant Functionsynonymous_variant

Allele frequency in gnomAD - whole
population

0.5882

Allele frequency in gnomAD - East Asian

0.39231000 Genomes Minor Allele

G

Uncontrolled when printed

37/79

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100

posi_con1000 Genomes Minor Allele Frequency

0.5775

SIFT Prediction-

dbSNP ID

rs3736455

ClinVar ID

166976

ClinVar Pathogenicity

BenignHGMD-

GEM-J WGA Allele Frequency

0.391

Report Inclusion

None

Variant (HGVSc)

NM_207352.4:c.823G>A

Gene Symbol

CYP4V2

Variant Type

SNV

Location

4:186201178-186201178

Exon Numbers

7/11

Ref

G

Alt

A

Frequency (Read)

1.0 (562/562)

Zygosity

Homozygous

Amino Acid Change (HGVSp)

NP_997235.3:p.Glu275Lys

User Classification

BenignACMG Classification

BenignACMG Labels

BS1(gnomAD),BS3(ClinVar),BP4(SIFT)

Inheritance Pattern

Recessive

Variant Function

missense_variant

Allele frequency in gnomAD - whole
population

0.02622

Allele frequency in gnomAD - East Asian

1.087E-4

1000 Genomes Minor Allele

A

1000 Genomes Minor Allele Frequency

0.0336

SIFT Prediction

tolerated

dbSNP ID

rs34745240

ClinVar ID

263298

ClinVar Pathogenicity

Benign/Likely_benign

HGMD

-

GEM-J WGA Allele Frequency-

Report Inclusion

None

Variant (HGVSc)

NM_024887.4:c.757G>A

Gene Symbol

DHDDS

Variant Type

SNV

Location

1:26460136-26460136

Exon Numbers

8/9

Ref

G

Alt

A

Frequency (Read)

0.47341 (365/771)

Zygosity

Heterozygous

Amino Acid Change (HGVSp)

NP_079163.2:p.Val253Met

User Classification

BenignACMG Classification

BenignACMG Labels

PP2(ClinVar),BA1(gnomAD),BS1(gnomAD),BS3(ClinVar),BP4(SIFT),BP6(Benign Variants from PMID:31213501)

Inheritance Pattern

Recessive

Variant Function

missense_variant

Allele frequency in gnomAD - whole
population

0.307

Allele frequency in gnomAD - East Asian

0.72591000 Genomes Minor Allele

A

1000 Genomes Minor Allele Frequency

0.4553

SIFT Prediction

tolerated

dbSNP ID

rs3816539

ClinVar ID

297075

ClinVar Pathogenicity

BenignHGMD-

GEM-J WGA Allele Frequency

0.773

Report Inclusion

None

Variant (HGVSc)

NM_178454.6:c.601-9A>G

Gene Symbol

DRAM2

Variant Type

SNV

Location

1:111118906-111118906

Exon Numbers

Intronic

Ref

T

Alt

C

Frequency (Read)

0.48493 (177/365)

Zygosity

Heterozygous

Amino Acid Change (HGVSp)-

Uncontrolled when printed

38/79

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User Classification

BenignACMG Classification

BenignACMG Labels

BA1(gnomAD),BS1(gnomAD),BS3(ClinVar)

Inheritance Pattern

Recessive

Variant Function

splice_polypyrimidine_tract_variant,intron_variant

Allele frequency in gnomAD - whole
population

0.2226

Allele frequency in gnomAD - East Asian

0.23991000 Genomes Minor Allele

C

1000 Genomes Minor Allele Frequency

0.3285

SIFT Prediction-

dbSNP ID

rs325917

ClinVar ID

677168

ClinVar Pathogenicity

BenignHGMD-

GEM-J WGA Allele Frequency

0.296

Report Inclusion

None

Variant (HGVSc)

NM_001292009.2:c.6977G>A

Gene Symbol

EYS

Variant Type

SNV

Location

6:63984461-63984461

Exon Numbers

35/44

Ref

C

Alt

T

Frequency (Read)

0.53099 (317/597)

Zygosity

Heterozygous

Amino Acid Change (HGVSp)

NP_001278938.1:p.Arg2326Gln

User Classification

BenignACMG Classification

BenignACMG Labels

PM5(ClinVar),PP3(SIFT),BA1(gnomAD),BS1(gnomAD),BS3(ClinVar),BP1(ClinVar),BP4(BLOSUM),BP6(Benign Variants from PMID:
31213501)

Inheritance Pattern

Recessive

Variant Function

missense_variant

Allele frequency in gnomAD - whole
population

0.3354

Allele frequency in gnomAD - East Asian

0.35251000 Genomes Minor Allele

T1000 Genomes Minor Allele Frequency

0.3496

SIFT Predictiondeleterious

dbSNP ID

rs4710457

ClinVar ID

93620

ClinVar Pathogenicity

BenignHGMD-

GEM-J WGA Allele Frequency

0.349

Report Inclusion

None

Variant (HGVSc)

NM_001292009.2:c.6079-4_6079-3delGene Symbol

EYS

Variant Type

Deletion

Location

6:64307084-64307086

Exon Numbers

Intronic

Ref

TGA

Alt

T

Frequency (Read)

0.49333 (148/300)

Zygosity

Heterozygous

Amino Acid Change (HGVSp)-

User Classification

BenignACMG Classification

BenignACMG Labels

BA1(gnomAD),BS1(gnomAD),BS3(ClinVar)

Inheritance Pattern

Recessive

Variant Function

splice_polypyrimidine_tract_variant,splice_region_variant,intron_variant

Allele frequency in gnomAD - whole
population

0.5506

Allele frequency in gnomAD - East Asian

0.50321000 Genomes Minor Allele-

1000 Genomes Minor Allele Frequency

0.6741

SIFT Prediction-

dbSNP ID

rs35395170

ClinVar ID

196616

ClinVar Pathogenicity

BenignHGMD-

GEM-J WGA Allele Frequency

0.51

Report Inclusion

None

Uncontrolled when printed

39/79

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105

posi_con

Variant (HGVSc)

NM_001292009.2:c.5705A>T

Gene Symbol

EYS

Variant Type

SNV

Location

6:64439292-64439292

Exon Numbers

27/44

Ref

T

Alt

A

Frequency (Read)

0.46 (184/400)

Zygosity

Heterozygous

Amino Acid Change (HGVSp)

NP_001278938.1:p.Asn1902Ile

User Classification

BenignACMG Classification

BenignACMG Labels

PP3(BLOSUM),BA1(gnomAD),BS1(gnomAD),BS3(ClinVar),BP1(ClinVar),BP4(SIFT),BP6(Benign Variants from PMID:31213501)

Inheritance Pattern

Recessive

Variant Function

missense_variant

Allele frequency in gnomAD - whole
population

0.3047

Allele frequency in gnomAD - East Asian

0.48961000 Genomes Minor Allele

A

1000 Genomes Minor Allele Frequency

0.2913

SIFT Prediction

tolerated

dbSNP ID

rs9353806

ClinVar ID

137256

ClinVar Pathogenicity

BenignHGMD-

GEM-J WGA Allele Frequency

0.444

Report Inclusion

None

Variant (HGVSc)

NM_001292009.2:c.3444-5C>T

Gene Symbol

EYS

Variant Type

SNV

Location

6:64626250-64626250

Exon Numbers

Intronic

Ref

G

Alt

A

Frequency (Read)

0.44643 (100/224)

Zygosity

Heterozygous

Amino Acid Change (HGVSp)-

User Classification

BenignACMG Classification

BenignACMG Labels

BA1(gnomAD),BS1(gnomAD),BS3(ClinVar),BP4(dbscSNV),BP6(Benign Variants from PMID:31213501)

Inheritance Pattern

Recessive

Variant Function

splice_polypyrimidine_tract_variant,splice_region_variant,intron_variant

Allele frequency in gnomAD - whole
population

0.2252

Allele frequency in gnomAD - East Asian

0.33851000 Genomes Minor Allele

A

1000 Genomes Minor Allele Frequency

0.1955

SIFT Prediction-

dbSNP ID

rs9445051

ClinVar ID

357717

ClinVar Pathogenicity

BenignHGMD-

GEM-J WGA Allele Frequency

0.303

Report Inclusion

None

Variant (HGVSc)

NM_001292009.2:c.2555T>C

Gene Symbol

EYS

Variant Type

SNV

Location

6:64912570-64912570

Exon Numbers

16/44

Ref

A

Alt

G

Frequency (Read)

0.46196 (255/552)

Zygosity

Heterozygous

Amino Acid Change (HGVSp)

NP_001278938.1:p.Leu852Pro

User Classification

BenignACMG Classification

BenignACMG Labels

PP3(BLOSUM),BA1(gnomAD),BS1(gnomAD),BS3(ClinVar),BP1(ClinVar),BP4(SIFT),BP6(Benign Variants from PMID:31213501)

Inheritance Pattern

Recessive

Variant Function

missense_variant

Allele frequency in gnomAD - whole
population

0.593

Allele frequency in gnomAD - East Asian

0.4017

Uncontrolled when printed

40/79

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108

posi_con1000 Genomes Minor Allele

G

1000 Genomes Minor Allele Frequency

0.6464

SIFT Prediction

tolerated

dbSNP ID

rs9294631

ClinVar ID

93605

ClinVar Pathogenicity

BenignHGMD-

GEM-J WGA Allele Frequency

0.458

Report Inclusion

None

Variant (HGVSc)

NM_001292009.2:c.1891G>A

Gene Symbol

EYS

Variant Type

SNV

Location

6:65295995-65295995

Exon Numbers

12/44

Ref

C

Alt

T

Frequency (Read)

1.0 (548/548)

Zygosity

Homozygous

Amino Acid Change (HGVSp)

NP_001278938.1:p.Gly631Ser

User Classification

BenignACMG Classification

BenignACMG Labels

BA1(gnomAD),BS1(gnomAD),BS3(ClinVar),BP1(ClinVar),BP4(SIFT),BP6(Benign Variants from PMID:31213501)

Inheritance Pattern

Recessive

Variant Function

missense_variant

Allele frequency in gnomAD - whole
population

0.6246

Allele frequency in gnomAD - East Asian

0.917

1000 Genomes Minor Allele

T1000 Genomes Minor Allele Frequency

0.595

SIFT Prediction

tolerated

dbSNP ID

rs9342464

ClinVar ID

137267

ClinVar Pathogenicity

BenignHGMD-

GEM-J WGA Allele Frequency

0.893

Report Inclusion

None

Variant (HGVSc)

NM_001292009.2:c.1809C>T

Gene Symbol

EYS

Variant Type

SNV

Location

6:65296077-65296077

Exon Numbers

12/44

Ref

G

Alt

A

Frequency (Read)

1.0 (358/358)

Zygosity

Homozygous

Amino Acid Change (HGVSp)

NP_001278938.1:p.Val603=

User Classification

BenignACMG Classification

BenignACMG Labels

BA1(gnomAD),BS1(gnomAD),BS3(ClinVar),BP7(VEP,dbscSNV,GERP)

Inheritance Pattern

Recessive

Variant Functionsynonymous_variant

Allele frequency in gnomAD - whole
population

0.625

Allele frequency in gnomAD - East Asian

0.91741000 Genomes Minor Allele

A

1000 Genomes Minor Allele Frequency

0.5948SIFT Prediction-

dbSNP ID

rs9345601

ClinVar ID

137266

ClinVar Pathogenicity

Benign/Likely_benign

HGMD

-

GEM-J WGA Allele Frequency

0.894

Report Inclusion

None

Variant (HGVSc)

NM_001292009.2:c.1146T>C

Gene Symbol

EYS

Variant Type

SNV

Location

6:65402516-65402516

Exon Numbers

7/44

Ref

A

Alt

G

Frequency (Read)

0.45588 (124/272)

Zygosity

Heterozygous

Uncontrolled when printed

41/79

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posi_con

Amino Acid Change (HGVSp)

NP_001278938.1:p.Asn382=

User Classification

BenignACMG Classification

BenignACMG Labels

BA1(gnomAD),BS1(gnomAD),BS3(ClinVar),BP7(VEP,dbscSNV,GERP)

Inheritance Pattern

Recessive

Variant Functionsynonymous_variant

Allele frequency in gnomAD - whole
population

0.5195Allele frequency in gnomAD - East Asian

0.4431000 Genomes Minor Allele

G

1000 Genomes Minor Allele Frequency

0.506

SIFT Prediction-

dbSNP ID

rs974110

ClinVar ID

137262ClinVar Pathogenicity

BenignHGMD-

GEM-J WGA Allele Frequency

0.446

Report Inclusion

None

Variant (HGVSc)

NM_001292009.2:c.359C>T

Gene Symbol

EYS

Variant Type

SNV

Location

6:65495052-65495052

Exon Numbers

4/44

Ref

G

Alt

A

Frequency (Read)

0.49912 (284/569)

Zygosity

Heterozygous

Amino Acid Change (HGVSp)

NP_001278938.1:p.Thr120Met

User Classification

BenignACMG Classification

BenignACMG Labels

PP3(BLOSUM),BA1(gnomAD),BS1(gnomAD),BS3(ClinVar),BP1(ClinVar),BP4(SIFT),BP6(Benign Variants from PMID:31213501)

Inheritance Pattern

Recessive

Variant Function

missense_variant

Allele frequency in gnomAD - whole
population

0.2086

Allele frequency in gnomAD - East Asian

0.24681000 Genomes Minor Allele

A

1000 Genomes Minor Allele Frequency

0.1703

SIFT Prediction

tolerated_low_confidence

dbSNP ID

rs12193967

ClinVar ID

137261ClinVar Pathogenicity

BenignHGMD-

GEM-J WGA Allele Frequency

0.255

Report Inclusion

None

Variant (HGVSc)

NM_001201543.2:c.1212T>CGene Symbol

FAM161A

Variant Type

SNV

Location

2:61839792-61839792

Exon Numbers

3/7

Ref

A

Alt

G

Frequency (Read)

1.0 (727/727)

Zygosity

Homozygous

Amino Acid Change (HGVSp)

NP_001188472.1:p.Cys404=

User Classification

BenignACMG Classification

BenignACMG Labels

BA1(gnomAD),BS1(gnomAD),BS3(ClinVar),BP7(VEP,dbscSNV,GERP)

Inheritance Pattern

Recessive

Variant Functionsynonymous_variant

Allele frequency in gnomAD - whole
population

0.9756

Allele frequency in gnomAD - East Asian

0.99641000 Genomes Minor Allele

G

1000 Genomes Minor Allele Frequency

0.9796

SIFT Prediction-

dbSNP ID

rs4672457

ClinVar ID

96217

ClinVar Pathogenicity

BenignHGMD-

GEM-J WGA Allele Frequency

0.994

Report Inclusion

None

Uncontrolled when printed

42/79

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113

posi_con

Variant (HGVSc)

NM_001201543.2:c.706A>G

Gene Symbol

FAM161A

Variant Type

SNV

Location

2:61840298-61840298

Exon Numbers

3/7

Ref

T

Alt

C

Frequency (Read)

0.52802 (358/678)

Zygosity

Heterozygous

Amino Acid Change (HGVSp)

NP_001188472.1:p.Ile236Val

User Classification

BenignACMG Classification

BenignACMG Labels

BA1(gnomAD),BS1(gnomAD),BS3(ClinVar),BP1(ClinVar),BP4(SIFT),BP6(Benign Variants from PMID:31213501)

Inheritance Pattern

Recessive

Variant Function

missense_variant

Allele frequency in gnomAD - whole
population

0.1836

Allele frequency in gnomAD - East Asian

0.10531000 Genomes Minor Allele

C

1000 Genomes Minor Allele Frequency

0.1164

SIFT Prediction

tolerated

dbSNP ID

rs17513722

ClinVar ID

336742ClinVar Pathogenicity

BenignHGMD-

GEM-J WGA Allele Frequency

0.077

Report Inclusion

None

Variant (HGVSc)

NM_001201543.2:c.165T>G

Gene Symbol

FAM161A

Variant Type

SNV

Location

2:61853877-61853877

Exon Numbers

1/7

Ref

A

Alt

C

Frequency (Read)

1.0 (867/867)

Zygosity

Homozygous

Amino Acid Change (HGVSp)

NP_001188472.1:p.Ala55=

User Classification

BenignACMG Classification

BenignACMG Labels

BA1(gnomAD),BS1(gnomAD),BS3(ClinVar),BP7(VEP,dbscSNV,GERP)

Inheritance Pattern

Recessive

Variant Functionsynonymous_variant

Allele frequency in gnomAD - whole
population

0.9756

Allele frequency in gnomAD - East Asian

0.99671000 Genomes Minor Allele

C

1000 Genomes Minor Allele Frequency

0.9794

SIFT Prediction-

dbSNP ID

rs4270331

ClinVar ID

193466

ClinVar Pathogenicity

BenignHGMD-

GEM-J WGA Allele Frequency

0.994

Report Inclusion

None

Variant (HGVSc)

NM_000180.4:c.61T>C

Gene Symbol

GUCY2D

Variant Type

SNV

Location

17:8003108-8003108

Exon Numbers

2/20

Ref

T

Alt

C

Frequency (Read)

0.49822 (419/841)

Zygosity

Heterozygous

Amino Acid Change (HGVSp)

NP_000171.1:p.Trp21Arg

User Classification

BenignACMG Classification

BenignACMG Labels

PP2(ClinVar),PP3(BLOSUM),BS1(gnomAD),BS3(ClinVar),BP4(SIFT)

Inheritance Pattern

Recessive, DominantVariant Function

missense_variant

Allele frequency in gnomAD - whole
population

0.04798

Allele frequency in gnomAD - East Asian

0.02253

Uncontrolled when printed

43/79

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115

116

posi_con1000 Genomes Minor Allele

C

1000 Genomes Minor Allele Frequency

0.1226

SIFT Prediction

tolerated_low_confidence

dbSNP ID

rs9905402

ClinVar ID

92581

ClinVar Pathogenicity

BenignHGMD-

GEM-J WGA Allele Frequency

0.002747

Report Inclusion

None

Variant (HGVSc)

NM_000180.4:c.154G>T

Gene Symbol

GUCY2D

Variant Type

SNV

Location

17:8003201-8003201

Exon Numbers

2/20

Ref

G

Alt

T

Frequency (Read)

0.5286 (499/944)

Zygosity

Heterozygous

Amino Acid Change (HGVSp)

NP_000171.1:p.Ala52Ser

User Classification

BenignACMG Classification

BenignACMG Labels

PP2(ClinVar),BA1(gnomAD),BS1(gnomAD),BS3(ClinVar),BP4(SIFT)

Inheritance Pattern

Recessive, DominantVariant Function

missense_variant

Allele frequency in gnomAD - whole
population

0.4159Allele frequency in gnomAD - East Asian

0.69531000 Genomes Minor Allele

T1000 Genomes Minor Allele Frequency

0.4159SIFT Prediction

tolerated

dbSNP ID

rs61749665

ClinVar ID

9353

ClinVar Pathogenicity

BenignHGMD-

GEM-J WGA Allele Frequency

0.698

Report Inclusion

None

Variant (HGVSc)

NM_000180.4:c.2345T>A

Gene Symbol

GUCY2D

Variant Type

SNV

Location

17:8013961-8013961

Exon Numbers

12/20

Ref

T

Alt

A

Frequency (Read)

0.51165 (461/901)

Zygosity

Heterozygous

Amino Acid Change (HGVSp)

NP_000171.1:p.Leu782His

User Classification

BenignACMG Classification

BenignACMG Labels

PP2(ClinVar),PP3(BLOSUM),BA1(gnomAD),BS1(gnomAD),BS3(ClinVar),BP4(SIFT)

Inheritance Pattern

Recessive, DominantVariant Function

missense_variant

Allele frequency in gnomAD - whole
population

0.1228Allele frequency in gnomAD - East Asian

7.068E-4

1000 Genomes Minor Allele

A

1000 Genomes Minor Allele Frequency

0.1713

SIFT Prediction

tolerated

dbSNP ID

rs8069344

ClinVar ID

255475

ClinVar Pathogenicity

BenignHGMD-

GEM-J WGA Allele Frequency

1.328E-4

Report Inclusion

None

Variant (HGVSc)

NM_006899.5:c.118-3G>C

Gene Symbol

IDH3B

Variant Type

SNV

Location

20:2663761-2663761

Exon Numbers

Intronic

Ref

C

Alt

G

Frequency (Read)

1.0 (751/751)

Zygosity

Homozygous

Uncontrolled when printed

44/79

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posi_con

Amino Acid Change (HGVSp)-

User Classification

BenignACMG Classification

BenignACMG Labels

BA1(gnomAD),BS1(gnomAD),BS3(ClinVar),BP6(Benign Variants from PMID:31213501)

Inheritance Pattern

Recessive

Variant Function

splice_polypyrimidine_tract_variant,splice_region_variant,intron_variant

Allele frequency in gnomAD - whole
population

0.6896

Allele frequency in gnomAD - East Asian

0.61111000 Genomes Minor Allele

G

1000 Genomes Minor Allele Frequency

0.613

SIFT Prediction-

dbSNP ID

rs2073193

ClinVar ID

338028

ClinVar Pathogenicity

BenignHGMD-

GEM-J WGA Allele Frequency

0.568

Report Inclusion

None

Variant (HGVSc)

NM_000883.4:c.1575G>A

Gene Symbol

IMPDH1

Variant Type

SNV

Location

7:128394575-128394575

Exon Numbers

15/17

Ref

C

Alt

T

Frequency (Read)

0.4649 (351/755)

Zygosity

Heterozygous

Amino Acid Change (HGVSp)

NP_000874.2:p.Ala525=

User Classification

BenignACMG Classification

BenignACMG Labels

BA1(gnomAD),BS1(gnomAD),BS3(ClinVar),BP7(VEP,dbscSNV,GERP)

Inheritance Pattern

Recessive, DominantVariant Functionsynonymous_variant

Allele frequency in gnomAD - whole
population

0.2715Allele frequency in gnomAD - East Asian

0.36821000 Genomes Minor Allele

T1000 Genomes Minor Allele Frequency

0.2776

SIFT Prediction-

dbSNP ID

rs2228075

ClinVar ID

358873

ClinVar Pathogenicity

BenignHGMD-

GEM-J WGA Allele Frequency

0.346

Report Inclusion

None

Variant (HGVSc)

NM_016247.4:c.3381C>T

Gene Symbol

IMPG2

Variant Type

SNV

Location

3:101230998-101230998

Exon Numbers

16/19

Ref

G

Alt

A

Frequency (Read)

0.4901 (297/606)

Zygosity

Heterozygous

Amino Acid Change (HGVSp)

NP_057331.2:p.Leu1127=

User Classification

BenignACMG Classification

BenignACMG Labels

BA1(gnomAD),BS1(gnomAD),BS3(ClinVar),BP7(VEP,dbscSNV,GERP)

Inheritance Pattern

Recessive

Variant Functionsynonymous_variant

Allele frequency in gnomAD - whole
population

0.7909Allele frequency in gnomAD - East Asian

0.81451000 Genomes Minor Allele

A

1000 Genomes Minor Allele Frequency

0.8129SIFT Prediction-

dbSNP ID

rs348867

ClinVar ID

342337

ClinVar Pathogenicity

BenignHGMD-

GEM-J WGA Allele Frequency

0.755

Report Inclusion

None

Uncontrolled when printed

45/79

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121

posi_con

Variant (HGVSc)

NM_133497.4:c.183C>G

Gene Symbol

KCNV2

Variant Type

SNV

Location

9:2717922-2717922

Exon Numbers

1/2

Ref

C

Alt

G

Frequency (Read)

0.49948 (478/957)

Zygosity

Heterozygous

Amino Acid Change (HGVSp)

NP_598004.1:p.Gly61=

User Classification

BenignACMG Classification

BenignACMG Labels

BA1(gnomAD),BS1(gnomAD),BS3(ClinVar),BP7(VEP,dbscSNV,GERP)

Inheritance Pattern

Recessive

Variant Functionsynonymous_variant

Allele frequency in gnomAD - whole
population

0.6181Allele frequency in gnomAD - East Asian

0.78091000 Genomes Minor Allele

G

1000 Genomes Minor Allele Frequency

0.6603

SIFT Prediction-

dbSNP ID

rs10967705

ClinVar ID

96357

ClinVar Pathogenicity

BenignHGMD-

GEM-J WGA Allele Frequency

0.839

Report Inclusion

None

Variant (HGVSc)

NM_133497.4:c.795C>G

Gene Symbol

KCNV2

Variant Type

SNV

Location

9:2718534-2718534

Exon Numbers

1/2

Ref

C

Alt

G

Frequency (Read)

0.47128 (402/853)

Zygosity

Heterozygous

Amino Acid Change (HGVSp)

NP_598004.1:p.Ala265=

User Classification

BenignACMG Classification

BenignACMG Labels

BA1(gnomAD),BS1(gnomAD),BS3(ClinVar),BP7(VEP,dbscSNV,GERP)

Inheritance Pattern

Recessive

Variant Functionsynonymous_variant

Allele frequency in gnomAD - whole
population

0.4839Allele frequency in gnomAD - East Asian

0.71711000 Genomes Minor Allele

G

1000 Genomes Minor Allele Frequency

0.48

SIFT Prediction-

dbSNP ID

rs12237048

ClinVar ID

96362

ClinVar Pathogenicity

BenignHGMD-

GEM-J WGA Allele Frequency

0.75

Report Inclusion

None

Variant (HGVSc)

NM_001242957.3:c.1905T>CGene Symbol

MAK

Variant Type

SNV

Location

6:10764494-10764494

Exon Numbers

15/15

Ref

A

Alt

G

Frequency (Read)

0.51235 (332/648)

Zygosity

Heterozygous

Amino Acid Change (HGVSp)

NP_001229886.1:p.His635=

User Classification

BenignACMG Classification

BenignACMG Labels

BA1(gnomAD),BS1(gnomAD),BS3(ClinVar),BP7(VEP,dbscSNV,GERP)

Inheritance Pattern

Recessive

Variant Functionsynonymous_variant

Allele frequency in gnomAD - whole
population

0.8135Allele frequency in gnomAD - East Asian

0.9249Uncontrolled when printed

46/79

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posi_con1000 Genomes Minor Allele

G

1000 Genomes Minor Allele Frequency

0.8656

SIFT Prediction-

dbSNP ID

rs126405

ClinVar ID

354783

ClinVar Pathogenicity

BenignHGMD-

GEM-J WGA Allele Frequency

0.919

Report Inclusion

None

Variant (HGVSc)

NM_006343.3:c.1397G>A

Gene Symbol

MERTK

Variant Type

SNV

Location

2:111994351-111994351

Exon Numbers

9/19

Ref

G

Alt

A

Frequency (Read)

0.47089 (364/773)

Zygosity

Heterozygous

Amino Acid Change (HGVSp)

NP_006334.2:p.Arg466Lys

User Classification

BenignACMG Classification

BenignACMG Labels

BA1(gnomAD),BS1(gnomAD),BS3(ClinVar),BP1(ClinVar),BP4(SIFT),BP6(Benign Variants from PMID:31213501)

Inheritance Pattern

Recessive

Variant Function

missense_variant

Allele frequency in gnomAD - whole
population

0.5975Allele frequency in gnomAD - East Asian

0.24981000 Genomes Minor Allele

A

1000 Genomes Minor Allele Frequency

0.5615

SIFT Prediction

tolerated

dbSNP ID

rs7604639

ClinVar ID

330754

ClinVar Pathogenicity

BenignHGMD-

GEM-J WGA Allele Frequency

0.232

Report Inclusion

None

Variant (HGVSc)

NM_006343.3:c.1451-72G>T

Gene Symbol

MERTK

Variant Type

SNV

Location

2:111997251-111997251

Exon Numbers

Intronic

Ref

G

Alt

T

Frequency (Read)

0.45814 (197/430)

Zygosity

Heterozygous

Amino Acid Change (HGVSp)-

User Classification

BenignACMG Classification

BenignACMG Labels

BA1(gnomAD),BS1(gnomAD)

Inheritance Pattern

Recessive

Variant Function

intron_variant

Allele frequency in gnomAD - whole
population

0.323

Allele frequency in gnomAD - East Asian

0.10981000 Genomes Minor Allele

T1000 Genomes Minor Allele Frequency

0.3039SIFT Prediction-

dbSNP ID

rs3811632

ClinVar ID-

ClinVar Pathogenicity

-

HGMD

-

GEM-J WGA Allele Frequency

0.121

Report Inclusion

None

Variant (HGVSc)

NM_006343.3:c.1552A>G

Gene Symbol

MERTK

Variant Type

SNV

Location

2:111997424-111997424

Exon Numbers

10/19

Ref

A

Alt

G

Frequency (Read)

0.5 (338/676)

Zygosity

Heterozygous

Uncontrolled when printed

47/79

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posi_con

Amino Acid Change (HGVSp)

NP_006334.2:p.Ile518Val

User Classification

BenignACMG Classification

BenignACMG Labels

BA1(gnomAD),BS1(gnomAD),BS3(ClinVar),BP1(ClinVar),BP4(SIFT),BP6(Benign Variants from PMID:31213501)

Inheritance Pattern

Recessive

Variant Function

missense_variant

Allele frequency in gnomAD - whole
population

0.5976

Allele frequency in gnomAD - East Asian

0.24981000 Genomes Minor Allele

G

1000 Genomes Minor Allele Frequency

0.5615

SIFT Prediction

tolerated

dbSNP ID

rs2230515

ClinVar ID

330759ClinVar Pathogenicity

BenignHGMD-

GEM-J WGA Allele Frequency

0.232

Report Inclusion

None

Variant (HGVSc)

NM_006343.3:c.1881A>G

Gene Symbol

MERTK

Variant Type

SNV

Location

2:112008396-112008396

Exon Numbers

14/19

Ref

A

Alt

G

Frequency (Read)

0.47841 (277/579)

Zygosity

Heterozygous

Amino Acid Change (HGVSp)

NP_006334.2:p.Ser627=

User Classification

BenignACMG Classification

BenignACMG Labels

BA1(gnomAD),BS1(gnomAD),BS3(ClinVar),BP7(VEP,dbscSNV,GERP)

Inheritance Pattern

Recessive

Variant Functionsynonymous_variant

Allele frequency in gnomAD - whole
population

0.5853

Allele frequency in gnomAD - East Asian

0.2491000 Genomes Minor Allele

G

1000 Genomes Minor Allele Frequency

0.5152SIFT Prediction-

dbSNP ID

rs1131244

ClinVar ID

330762ClinVar Pathogenicity

BenignHGMD-

GEM-J WGA Allele Frequency

0.232

Report Inclusion

None

Variant (HGVSc)

NM_000260.4:c.3503+12_3503+33delGene Symbol

MYO7A

Variant Type

Deletion

Location

11:77184725-77184747

Exon Numbers

IntronicRef

GGGAGGCGGGGACACCAGGGCCTAlt

GFrequency (Read)

0.42934 (319/743)

Zygosity

Heterozygous

Amino Acid Change (HGVSp)-

User Classification

BenignACMG Classification

BenignACMG Labels

BA1(gnomAD),BS1(gnomAD),BS3(ClinVar)

Inheritance Pattern

Recessive

Variant Function

intron_variant

Allele frequency in gnomAD - whole
population

0.3798Allele frequency in gnomAD - East Asian

0.27091000 Genomes Minor Allele-

1000 Genomes Minor Allele Frequency-

SIFT Prediction-

dbSNP ID

rs111033223

ClinVar ID

43207

ClinVar Pathogenicity

BenignHGMD-

GEM-J WGA Allele Frequency

0.264

Report Inclusion

None

Uncontrolled when printed

48/79

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posi_con

Variant (HGVSc)

NM_000260.4:c.4996A>T

Gene Symbol

MYO7A

Variant Type

SNV

Location

11:77201591-77201591

Exon Numbers

36/49

Ref

A

Alt

T

Frequency (Read)

0.53571 (450/840)

Zygosity

Heterozygous

Amino Acid Change (HGVSp)

NP_000251.3:p.Ser1666Cys

User Classification

BenignACMG Classification

BenignACMG Labels

PP3(BLOSUM),BA1(gnomAD),BS1(gnomAD),BS3(ClinVar),BP1(ClinVar),BP4(SIFT)

Inheritance Pattern

Recessive

Variant Function

missense_variant

Allele frequency in gnomAD - whole
population

0.55

Allele frequency in gnomAD - East Asian

0.4881000 Genomes Minor Allele

T1000 Genomes Minor Allele Frequency

0.5517

SIFT Prediction

tolerated

dbSNP ID

rs2276288

ClinVar ID

43269

ClinVar Pathogenicity

BenignHGMD-

GEM-J WGA Allele Frequency

0.457

Report Inclusion

None

Variant (HGVSc)

NM_000260.4:c.5715A>G

Gene Symbol

MYO7A

Variant Type

SNV

Location

11:77206175-77206175

Exon Numbers

41/49

Ref

A

Alt

G

Frequency (Read)

0.52081 (388/745)

Zygosity

Heterozygous

Amino Acid Change (HGVSp)

NP_000251.3:p.Lys1905=

User Classification

BenignACMG Classification

BenignACMG Labels

BA1(gnomAD),BS1(gnomAD),BS3(ClinVar),BP7(VEP,dbscSNV,GERP)

Inheritance Pattern

Recessive

Variant Functionsynonymous_variant

Allele frequency in gnomAD - whole
population

0.5163

Allele frequency in gnomAD - East Asian

0.5091000 Genomes Minor Allele

G

1000 Genomes Minor Allele Frequency

0.5549SIFT Prediction-

dbSNP ID

rs2276293

ClinVar ID

43296

ClinVar Pathogenicity

BenignHGMD-

GEM-J WGA Allele Frequency

0.458

Report Inclusion

None

Variant (HGVSc)

NM_000260.4:c.5857-7A>T

Gene Symbol

MYO7A

Variant Type

SNV

Location

11:77208423-77208423

Exon Numbers

Intronic

Ref

A

Alt

T

Frequency (Read)

0.47047 (239/508)

Zygosity

Heterozygous

Amino Acid Change (HGVSp)-

User Classification

BenignACMG Classification

BenignACMG Labels

BA1(gnomAD),BS1(gnomAD),BS3(ClinVar),BP4(dbscSNV)

Inheritance Pattern

Recessive

Variant Function

splice_polypyrimidine_tract_variant,splice_region_variant,intron_variant

Allele frequency in gnomAD - whole
population

0.5621Allele frequency in gnomAD - East Asian

0.5047

Uncontrolled when printed

49/79

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132

posi_con1000 Genomes Minor Allele

T1000 Genomes Minor Allele Frequency

0.513

SIFT Prediction-

dbSNP ID

rs1320703

ClinVar ID

43303

ClinVar Pathogenicity

BenignHGMD-

GEM-J WGA Allele Frequency

0.457

Report Inclusion

None

Variant (HGVSc)

NM_000260.4:c.5860C>A

Gene Symbol

MYO7A

Variant Type

SNV

Location

11:77208433-77208433

Exon Numbers

43/49

Ref

C

Alt

A

Frequency (Read)

0.48905 (268/548)

Zygosity

Heterozygous

Amino Acid Change (HGVSp)

NP_000251.3:p.Leu1954Ile

User Classification

BenignACMG Classification

BenignACMG Labels

BA1(gnomAD),BS1(gnomAD),BS3(ClinVar),BP1(ClinVar),BP4(SIFT)

Inheritance Pattern

Recessive

Variant Function

missense_variant

Allele frequency in gnomAD - whole
population

0.4738Allele frequency in gnomAD - East Asian

0.35491000 Genomes Minor Allele

A

1000 Genomes Minor Allele Frequency

0.499

SIFT Prediction

tolerated

dbSNP ID

rs948962

ClinVar ID

43304

ClinVar Pathogenicity

BenignHGMD-

GEM-J WGA Allele Frequency

0.295

Report Inclusion

None

Variant (HGVSc)

NM_000260.4:c.6063G>A

Gene Symbol

MYO7A

Variant Type

SNV

Location

11:77211163-77211163

Exon Numbers

45/49

Ref

G

Alt

A

Frequency (Read)

0.54068 (412/762)

Zygosity

Heterozygous

Amino Acid Change (HGVSp)

NP_000251.3:p.Lys2021=

User Classification

BenignACMG Classification

BenignACMG Labels

BS1(gnomAD),BS3(ClinVar),BP7(VEP,dbscSNV,GERP)

Inheritance Pattern

Recessive

Variant Functionsynonymous_variant

Allele frequency in gnomAD - whole
population

0.00673

Allele frequency in gnomAD - East Asian

0.01000 Genomes Minor Allele

A

1000 Genomes Minor Allele Frequency

0.0309SIFT Prediction-

dbSNP ID

rs111033209

ClinVar ID

43317

ClinVar Pathogenicity

BenignHGMD-

GEM-J WGA Allele Frequency

1.323E-4

Report Inclusion

None

Variant (HGVSc)

NM_000283.4:c.958G>A

Gene Symbol

PDE6B

Variant Type

SNV

Location

4:654854-654854

Exon Numbers

6/22

Ref

G

Alt

A

Frequency (Read)

1.0 (585/585)

Zygosity

Homozygous

Uncontrolled when printed

50/79

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posi_con

Amino Acid Change (HGVSp)

NP_000274.3:p.Val320Ile

User Classification

BenignACMG Classification

BenignACMG Labels

BA1(gnomAD),BS1(gnomAD),BS3(ClinVar),BP1(ClinVar),BP4(SIFT)

Inheritance Pattern

Recessive, DominantVariant Function

missense_variant

Allele frequency in gnomAD - whole
population

0.9998Allele frequency in gnomAD - East Asian

1.01000 Genomes Minor Allele

A

1000 Genomes Minor Allele Frequency

0.999

SIFT Prediction

tolerated

dbSNP ID

rs10902758

ClinVar ID

167436

ClinVar Pathogenicity

BenignHGMD-

GEM-J WGA Allele Frequency

1.0

Report Inclusion

None

Variant (HGVSc)

NM_006204.4:c.252G>A

Gene Symbol

PDE6C

Variant Type

SNV

Location

10:93612977-93612977

Exon Numbers

1/22

Ref

G

Alt

A

Frequency (Read)

0.49032 (380/775)

Zygosity

Heterozygous

Amino Acid Change (HGVSp)

NP_006195.3:p.Leu84=

User Classification

BenignACMG Classification

BenignACMG Labels

BA1(gnomAD),BS1(gnomAD),BS3(ClinVar),BP7(VEP,dbscSNV,GERP)

Inheritance Pattern

Recessive

Variant Functionsynonymous_variant

Allele frequency in gnomAD - whole
population

0.162

Allele frequency in gnomAD - East Asian

0.11141000 Genomes Minor Allele

A

1000 Genomes Minor Allele Frequency

0.1643

SIFT Prediction-

dbSNP ID

rs1131978

ClinVar ID

95346

ClinVar Pathogenicity

BenignHGMD-

GEM-J WGA Allele Frequency

0.084

Report Inclusion

None

Variant (HGVSc)

NM_006204.4:c.282C>T

Gene Symbol

PDE6C

Variant Type

SNV

Location

10:93613007-93613007

Exon Numbers

1/22

Ref

C

Alt

T

Frequency (Read)

0.49486 (385/778)

Zygosity

Heterozygous

Amino Acid Change (HGVSp)

NP_006195.3:p.Asp94=

User Classification

BenignACMG Classification

BenignACMG Labels

BA1(gnomAD),BS1(gnomAD),BS3(ClinVar),BP7(VEP,dbscSNV,GERP)

Inheritance Pattern

Recessive

Variant Functionsynonymous_variant

Allele frequency in gnomAD - whole
population

0.07892

Allele frequency in gnomAD - East Asian

3.263E-4

1000 Genomes Minor Allele

T1000 Genomes Minor Allele Frequency

0.0429SIFT Prediction-

dbSNP ID

rs12781149

ClinVar ID

95347

ClinVar Pathogenicity

BenignHGMD-

GEM-J WGA Allele Frequency

6.609E-4

Report Inclusion

None

Uncontrolled when printed

51/79

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137

posi_con

Variant (HGVSc)

NM_006204.4:c.1270-7A>G

Gene Symbol

PDE6C

Variant Type

SNV

Location

10:93635490-93635490

Exon Numbers

Intronic

Ref

A

Alt

G

Frequency (Read)

1.0 (280/280)

Zygosity

Homozygous

Amino Acid Change (HGVSp)-

User Classification

BenignACMG Classification

BenignACMG Labels

BA1(gnomAD),BS1(gnomAD),BS3(ClinVar),BP4(dbscSNV)

Inheritance Pattern

Recessive

Variant Function

splice_region_variant,splice_polypyrimidine_tract_variant,intron_variant

Allele frequency in gnomAD - whole
population

0.7329Allele frequency in gnomAD - East Asian

0.65921000 Genomes Minor Allele

G

1000 Genomes Minor Allele Frequency

0.7288SIFT Prediction-

dbSNP ID

rs616522

ClinVar ID

259940

ClinVar Pathogenicity

BenignHGMD-

GEM-J WGA Allele Frequency

0.643

Report Inclusion

None

Variant (HGVSc)

NM_006204.4:c.1935+10C>A

Gene Symbol

PDE6C

Variant Type

SNV

Location

10:93646057-93646057

Exon Numbers

Intronic

Ref

C

Alt

A

Frequency (Read)

0.48871 (303/620)

Zygosity

Heterozygous

Amino Acid Change (HGVSp)-

User Classification

BenignACMG Classification

BenignACMG Labels

BA1(gnomAD),BS1(gnomAD),BS3(ClinVar)

Inheritance Pattern

Recessive

Variant Function

intron_variant

Allele frequency in gnomAD - whole
population

0.4568Allele frequency in gnomAD - East Asian

0.40631000 Genomes Minor Allele

A

1000 Genomes Minor Allele Frequency

0.4133

SIFT Prediction-

dbSNP ID

rs1409332

ClinVar ID

259943

ClinVar Pathogenicity

BenignHGMD-

GEM-J WGA Allele Frequency

0.447

Report Inclusion

None

Variant (HGVSc)

NM_172240.3:c.453-12_453-3delGene Symbol

POC1B

Variant Type

Deletion

Location

12:89472277-89472287

Exon Numbers

Intronic

Ref

TAGAAAGAAGA

Alt

T

Frequency (Read)

0.40476 (68/168)

Zygosity

Heterozygous

Amino Acid Change (HGVSp)-

User Classification

BenignACMG Classification

BenignACMG Labels

BA1(gnomAD),BS1(gnomAD),BS3(ClinVar)

Inheritance Pattern

Recessive

Variant Function

splice_polypyrimidine_tract_variant,splice_region_variant,intron_variant

Allele frequency in gnomAD - whole
population

0.4817

Allele frequency in gnomAD - East Asian

0.5622

Uncontrolled when printed

52/79

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posi_con1000 Genomes Minor Allele-

1000 Genomes Minor Allele Frequency

0.5399SIFT Prediction-

dbSNP ID

rs59139895

ClinVar ID

677291ClinVar Pathogenicity

BenignHGMD-

GEM-J WGA Allele Frequency

0.699

Report Inclusion

None

Variant (HGVSc)

NM_006017.3:c.2374-6T>C

Gene Symbol

PROM1

Variant Type

SNV

Location

4:15980543-15980543

Exon Numbers

Intronic

Ref

A

Alt

G

Frequency (Read)

0.51039 (172/337)

Zygosity

Heterozygous

Amino Acid Change (HGVSp)-

User Classification

BenignACMG Classification

BenignACMG Labels

BA1(gnomAD),BS1(gnomAD),BS3(ClinVar),BP4(dbscSNV)

Inheritance Pattern

Recessive, DominantVariant Function

splice_polypyrimidine_tract_variant,splice_region_variant,intron_variant

Allele frequency in gnomAD - whole
population

0.3905Allele frequency in gnomAD - East Asian

0.17371000 Genomes Minor Allele

G

1000 Genomes Minor Allele Frequency

0.4469SIFT Prediction-

dbSNP ID

rs6449209

ClinVar ID

95334

ClinVar Pathogenicity

BenignHGMD-

GEM-J WGA Allele Frequency

0.225

Report Inclusion

None

Variant (HGVSc)

NM_006017.3:c.303+6G>A

Gene Symbol

PROM1

Variant Type

SNV

Location

4:16035729-16035729

Exon Numbers

Intronic

Ref

C

Alt

T

Frequency (Read)

0.49471 (234/473)

Zygosity

Heterozygous

Amino Acid Change (HGVSp)-

User Classification

BenignACMG Classification

BenignACMG Labels

BA1(gnomAD),BS1(gnomAD),BS3(ClinVar)

Inheritance Pattern

Recessive, DominantVariant Function

splice_donor_region_variant,intron_variant

Allele frequency in gnomAD - whole
population

0.4489Allele frequency in gnomAD - East Asian

0.14881000 Genomes Minor Allele

T1000 Genomes Minor Allele Frequency

0.2961

SIFT Prediction-

dbSNP ID

rs2078622

ClinVar ID

259906

ClinVar Pathogenicity

BenignHGMD-

GEM-J WGA Allele Frequency

0.219

Report Inclusion

None

Variant (HGVSc)

NM_000322.5:c.1013A>G

Gene Symbol

PRPH2

Variant Type

SNV

Location

6:42698323-42698323

Exon Numbers

3/3

Ref

T

Alt

C

Frequency (Read)

0.51499 (378/734)

Zygosity

Heterozygous

Uncontrolled when printed

53/79

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posi_con

Amino Acid Change (HGVSp)

NP_000313.2:p.Asp338Gly

User Classification

BenignACMG Classification

BenignACMG Labels

PP2(ClinVar),PP3(BLOSUM),BA1(gnomAD),BS1(gnomAD),BS3(ClinVar),BP4(SIFT),BP6(Benign Variants from PMID:31213501)

Inheritance Pattern

Recessive, DominantVariant Function

missense_variant

Allele frequency in gnomAD - whole
population

0.7761Allele frequency in gnomAD - East Asian

0.86161000 Genomes Minor Allele

C

1000 Genomes Minor Allele Frequency

0.7574

SIFT Prediction

tolerated

dbSNP ID

rs434102

ClinVar ID

138906

ClinVar Pathogenicity

BenignHGMD-

GEM-J WGA Allele Frequency

0.841

Report Inclusion

None

Variant (HGVSc)

NM_000322.5:c.929G>A

Gene Symbol

PRPH2

Variant Type

SNV

Location

6:42698407-42698407

Exon Numbers

3/3

Ref

C

Alt

T

Frequency (Read)

0.50628 (484/956)

Zygosity

Heterozygous

Amino Acid Change (HGVSp)

NP_000313.2:p.Arg310Lys

User Classification

BenignACMG Classification

BenignACMG Labels

PP2(ClinVar),BA1(gnomAD),BS1(gnomAD),BS3(ClinVar),BP4(SIFT),BP6(Benign Variants from PMID:31213501)

Inheritance Pattern

Recessive, DominantVariant Function

missense_variant

Allele frequency in gnomAD - whole
population

0.9123

Allele frequency in gnomAD - East Asian

0.9981000 Genomes Minor Allele

T1000 Genomes Minor Allele Frequency

0.9413

SIFT Prediction

tolerated

dbSNP ID

rs425876

ClinVar ID

138905

ClinVar Pathogenicity

BenignHGMD-

GEM-J WGA Allele Frequency

0.999

Report Inclusion

None

Variant (HGVSc)

NM_000322.5:c.910C>G

Gene Symbol

PRPH2

Variant Type

SNV

Location

6:42698426-42698426

Exon Numbers

3/3

Ref

G

Alt

C

Frequency (Read)

0.49948 (480/961)

Zygosity

Heterozygous

Amino Acid Change (HGVSp)

NP_000313.2:p.Gln304Glu

User Classification

BenignACMG Classification

BenignACMG Labels

PP2(ClinVar),BA1(gnomAD),BS1(gnomAD),BS3(ClinVar),BP4(SIFT),BP6(Benign Variants from PMID:31213501)

Inheritance Pattern

Recessive, DominantVariant Function

missense_variant

Allele frequency in gnomAD - whole
population

0.7749Allele frequency in gnomAD - East Asian

0.86061000 Genomes Minor Allele

C

1000 Genomes Minor Allele Frequency

0.7566

SIFT Prediction

tolerated

dbSNP ID

rs390659

ClinVar ID

138904

ClinVar Pathogenicity

BenignHGMD-

GEM-J WGA Allele Frequency

0.839

Report Inclusion

None

Uncontrolled when printed

54/79

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posi_con

Variant (HGVSc)

NM_000322.5:c.318T>C

Gene Symbol

PRPH2

Variant Type

SNV

Location

6:42722017-42722017

Exon Numbers

1/3

Ref

A

Alt

G

Frequency (Read)

0.49612 (447/901)

Zygosity

Heterozygous

Amino Acid Change (HGVSp)

NP_000313.2:p.Val106=

User Classification

BenignACMG Classification

BenignACMG Labels

BA1(gnomAD),BS1(gnomAD),BS3(ClinVar),BP7(VEP,dbscSNV,GERP)

Inheritance Pattern

Recessive, DominantVariant Functionsynonymous_variant

Allele frequency in gnomAD - whole
population

0.5776

Allele frequency in gnomAD - East Asian

0.58971000 Genomes Minor Allele

G

1000 Genomes Minor Allele Frequency

0.5845

SIFT Prediction-

dbSNP ID

rs7764439

ClinVar ID

92846

ClinVar Pathogenicity

BenignHGMD-

GEM-J WGA Allele Frequency

0.469

Report Inclusion

None

Variant (HGVSc)

NM_002905.5:c.423C>T

Gene Symbol

RDH5

Variant Type

SNV

Location

12:55721801-55721801

Exon Numbers

3/5

Ref

C

Alt

T

Frequency (Read)

0.51348 (457/890)

Zygosity

Heterozygous

Amino Acid Change (HGVSp)

NP_002896.2:p.Ile141=

User Classification

BenignACMG Classification

BenignACMG Labels

BA1(gnomAD),BS1(gnomAD),BS3(ClinVar),BP7(VEP,dbscSNV,GERP)

Inheritance Pattern

Recessive

Variant Functionsynonymous_variant

Allele frequency in gnomAD - whole
population

0.1905Allele frequency in gnomAD - East Asian

0.11651000 Genomes Minor Allele

T1000 Genomes Minor Allele Frequency

0.1528SIFT Prediction-

dbSNP ID

rs3138142

ClinVar ID

258857

ClinVar Pathogenicity

BenignHGMD-

GEM-J WGA Allele Frequency

0.052

Report Inclusion

None

Variant (HGVSc)

NM_207391.3:c.286G>T

Gene Symbol

RGS9BP

Variant Type

SNV

Location

19:32676549-32676549

Exon Numbers

1/1

Ref

G

Alt

T

Frequency (Read)

0.48469 (459/947)

Zygosity

Heterozygous

Amino Acid Change (HGVSp)

NP_997274.2:p.Ala96Ser

User Classification

BenignACMG Classification

BenignACMG Labels

BA1(gnomAD),BS1(gnomAD),BS3(ClinVar),BP4(SIFT)

Inheritance Pattern

Recessive

Variant Function

missense_variant

Allele frequency in gnomAD - whole
population

0.5934

Allele frequency in gnomAD - East Asian

0.3218Uncontrolled when printed

55/79

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posi_con1000 Genomes Minor Allele

T1000 Genomes Minor Allele Frequency

0.4349SIFT Prediction

tolerated

dbSNP ID

rs259290

ClinVar ID

96676

ClinVar Pathogenicity

BenignHGMD-

GEM-J WGA Allele Frequency

0.278

Report Inclusion

None

Variant (HGVSc)

NM_207391.3:c.*2G>A

Gene Symbol

RGS9BP

Variant Type

SNV

Location

19:32676973-32676973

Exon Numbers

1/1

Ref

G

Alt

A

Frequency (Read)

0.46315 (421/909)

Zygosity

Heterozygous

Amino Acid Change (HGVSp)-

User Classification

BenignACMG Classification

BenignACMG Labels

BA1(gnomAD),BS1(gnomAD),BP6(ClinVar)

Inheritance Pattern

Recessive

Variant Function

3_prime_UTR_variant

Allele frequency in gnomAD - whole
population

0.6032

Allele frequency in gnomAD - East Asian

0.31221000 Genomes Minor Allele

A

1000 Genomes Minor Allele Frequency

0.5373

SIFT Prediction-

dbSNP ID

rs259291

ClinVar ID

167597

ClinVar Pathogenicity

BenignHGMD-

GEM-J WGA Allele Frequency

0.362

Report Inclusion

None

Variant (HGVSc)

NM_000539.3:c.696+4C>T

Gene Symbol

RHO

Variant Type

SNV

Location

3:129532420-129532420

Exon Numbers

Intronic

Ref

C

Alt

T

Frequency (Read)

0.47076 (330/701)

Zygosity

Heterozygous

Amino Acid Change (HGVSp)-

User Classification

BenignACMG Classification

BenignACMG Labels

BA1(gnomAD),BS1(gnomAD),BS3(ClinVar),BP6(Benign Variants from PMID:31213501)

Inheritance Pattern

Recessive, DominantVariant Function

splice_donor_region_variant,intron_variant

Allele frequency in gnomAD - whole
population

0.08151

Allele frequency in gnomAD - East Asian

0.063361000 Genomes Minor Allele

T1000 Genomes Minor Allele Frequency

0.0857

SIFT Prediction-

dbSNP ID

rs56340615

ClinVar ID

256384

ClinVar Pathogenicity

BenignHGMD-

GEM-J WGA Allele Frequency

0.039

Report Inclusion

None

Variant (HGVSc)

NM_000327.4:c.353G>C

Gene Symbol

ROM1

Variant Type

SNV

Location

11:62613634-62613634

Exon Numbers

1/3

Ref

G

Alt

C

Frequency (Read)

1.0 (1121/1121)

Zygosity

Homozygous

Uncontrolled when printed

56/79

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posi_con

Amino Acid Change (HGVSp)

NP_000318.2:p.Gly118Ala

User Classification

BenignACMG Classification

BenignACMG Labels

BA1(gnomAD),BS1(gnomAD),BS3(ClinVar),BP4(SIFT)

Inheritance Pattern

Dominant

Variant Function

missense_variant

Allele frequency in gnomAD - whole
population

0.9847

Allele frequency in gnomAD - East Asian

0.99941000 Genomes Minor Allele

C

1000 Genomes Minor Allele Frequency

0.9353

SIFT Prediction

tolerated

dbSNP ID

rs1799959

ClinVar ID

167600

ClinVar Pathogenicity

BenignHGMD-

GEM-J WGA Allele Frequency

1.0

Report Inclusion

None

Variant (HGVSc)

NM_006269.2:c.2615G>A

Gene Symbol

RP1

Variant Type

SNV

Location

8:54626497-54626497

Exon Numbers

4/4

Ref

G

Alt

A

Frequency (Read)

0.44828 (195/435)

Zygosity

Heterozygous

Amino Acid Change (HGVSp)

NP_006260.1:p.Arg872His

User Classification

BenignACMG Classification

BenignACMG Labels

PP3(SIFT),BA1(gnomAD),BS1(gnomAD),BS3(ClinVar),BP1(ClinVar),BP6(Benign Variants from PMID:31213501)

Inheritance Pattern

Recessive, DominantVariant Function

missense_variant

Allele frequency in gnomAD - whole
population

0.2761Allele frequency in gnomAD - East Asian

0.44081000 Genomes Minor Allele

A

1000 Genomes Minor Allele Frequency

0.2722SIFT Predictiondeleterious

dbSNP ID

rs444772

ClinVar ID

167602ClinVar Pathogenicity

BenignHGMD-

GEM-J WGA Allele Frequency

0.391

Report Inclusion

None

Variant (HGVSc)

NM_006269.2:c.2953A>T

Gene Symbol

RP1

Variant Type

SNV

Location

8:54626835-54626835

Exon Numbers

4/4

Ref

A

Alt

T

Frequency (Read)

0.52941 (216/408)

Zygosity

Heterozygous

Amino Acid Change (HGVSp)

NP_006260.1:p.Asn985Tyr

User Classification

BenignACMG Classification

BenignACMG Labels

PP3(SIFT),BA1(gnomAD),BS1(gnomAD),BS3(ClinVar),BP1(ClinVar),BP6(Benign Variants from PMID:31213501)

Inheritance Pattern

Recessive, DominantVariant Function

missense_variant

Allele frequency in gnomAD - whole
population

0.3433

Allele frequency in gnomAD - East Asian

0.06062

1000 Genomes Minor Allele

T1000 Genomes Minor Allele Frequency

0.25

SIFT Predictiondeleterious

dbSNP ID

rs2293869

ClinVar ID

5969

ClinVar Pathogenicity

Benign/Likely_benign

HGMD

-

GEM-J WGA Allele Frequency

0.107

Report Inclusion

None

Uncontrolled when printed

57/79

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posi_con

Variant (HGVSc)

NM_006269.2:c.3699C>T

Gene Symbol

RP1

Variant Type

SNV

Location

8:54627581-54627581

Exon Numbers

4/4

Ref

C

Alt

T

Frequency (Read)

0.44444 (304/684)

Zygosity

Heterozygous

Amino Acid Change (HGVSp)

NP_006260.1:p.Ser1233=

User Classification

BenignACMG Classification

BenignACMG Labels

BS1(gnomAD),BS3(ClinVar),BP7(VEP,dbscSNV,GERP)

Inheritance Pattern

Recessive, DominantVariant Functionsynonymous_variant

Allele frequency in gnomAD - whole
population

0.01618

Allele frequency in gnomAD - East Asian

0.01000 Genomes Minor Allele

T1000 Genomes Minor Allele Frequency

0.0234

SIFT Prediction-

dbSNP ID

rs114557304

ClinVar ID

363293

ClinVar Pathogenicity

BenignHGMD-

GEM-J WGA Allele Frequency-

Report Inclusion

None

Variant (HGVSc)

NM_006269.2:c.4784G>A

Gene Symbol

RP1

Variant Type

SNV

Location

8:54628666-54628666

Exon Numbers

4/4

Ref

G

Alt

A

Frequency (Read)

0.45597 (233/511)

Zygosity

Heterozygous

Amino Acid Change (HGVSp)

NP_006260.1:p.Arg1595Gln

User Classification

BenignACMG Classification

BenignACMG Labels

PP3(SIFT),BS1(gnomAD),BS3(ClinVar),BP1(ClinVar),BP4(BLOSUM)

Inheritance Pattern

Recessive, DominantVariant Function

missense_variant

Allele frequency in gnomAD - whole
population

0.0164

Allele frequency in gnomAD - East Asian

1.088E-4

1000 Genomes Minor Allele

A

1000 Genomes Minor Allele Frequency

0.0242SIFT Predictiondeleterious

dbSNP ID

rs35084330

ClinVar ID

363303

ClinVar Pathogenicity

BenignHGMD-

GEM-J WGA Allele Frequency

6.581E-5

Report Inclusion

None

Variant (HGVSc)

NM_006269.2:c.5071T>C

Gene Symbol

RP1

Variant Type

SNV

Location

8:54628953-54628953

Exon Numbers

4/4

Ref

T

Alt

C

Frequency (Read)

0.46374 (275/593)

Zygosity

Heterozygous

Amino Acid Change (HGVSp)

NP_006260.1:p.Ser1691Pro

User Classification

BenignACMG Classification

BenignACMG Labels

PP3(BLOSUM),BA1(gnomAD),BS1(gnomAD),BS3(ClinVar),BP1(ClinVar),BP4(SIFT),BP6(Benign Variants from PMID:31213501)

Inheritance Pattern

Recessive, DominantVariant Function

missense_variant

Allele frequency in gnomAD - whole
population

0.2775Allele frequency in gnomAD - East Asian

0.4413

Uncontrolled when printed

58/79

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156

posi_con1000 Genomes Minor Allele

C

1000 Genomes Minor Allele Frequency

0.279

SIFT Prediction

tolerated

dbSNP ID

rs414352

ClinVar ID

95354

ClinVar Pathogenicity

BenignHGMD-

GEM-J WGA Allele Frequency

0.391

Report Inclusion

None

Variant (HGVSc)

NM_006269.2:c.6098G>A

Gene Symbol

RP1

Variant Type

SNV

Location

8:54629980-54629980

Exon Numbers

4/4

Ref

G

Alt

A

Frequency (Read)

0.43155 (145/336)

Zygosity

Heterozygous

Amino Acid Change (HGVSp)

NP_006260.1:p.Cys2033Tyr

User Classification

BenignACMG Classification

BenignACMG Labels

PP3(BLOSUM),BA1(gnomAD),BS1(gnomAD),BS3(ClinVar),BP1(ClinVar),BP4(SIFT)

Inheritance Pattern

Recessive, DominantVariant Function

missense_variant

Allele frequency in gnomAD - whole
population

0.3354

Allele frequency in gnomAD - East Asian

0.06062

1000 Genomes Minor Allele

A

1000 Genomes Minor Allele Frequency

0.2157

SIFT Prediction

tolerated

dbSNP ID

rs61739567

ClinVar ID

95357

ClinVar Pathogenicity

Benign/Likely_benign

HGMD

-

GEM-J WGA Allele Frequency

0.107

Report Inclusion

None

Variant (HGVSc)

NM_178857.6:c.6853G>A

Gene Symbol

RP1L1

Variant Type

SNV

Location

8:10607245-10607245

Exon Numbers

4/4

Ref

C

Alt

T

Frequency (Read)

0.50185 (408/813)

Zygosity

Heterozygous

Amino Acid Change (HGVSp)

NP_849188.4:p.Gly2285Arg

User Classification

BenignACMG Classification

BenignACMG Labels

PP3(SIFT),BA1(gnomAD),BS1(gnomAD),BS3(ClinVar),BP1(ClinVar),BP6(Benign Variants from PMID:31213501)

Inheritance Pattern

Recessive, DominantVariant Function

missense_variant

Allele frequency in gnomAD - whole
population

0.4784

Allele frequency in gnomAD - East Asian

0.56221000 Genomes Minor Allele

T1000 Genomes Minor Allele Frequency

0.472

SIFT Predictiondeleterious

dbSNP ID

rs55642448

ClinVar ID

361209ClinVar Pathogenicity

BenignHGMD-

GEM-J WGA Allele Frequency

0.526

Report Inclusion

None

Variant (HGVSc)

NM_178857.6:c.6723A>G

Gene Symbol

RP1L1

Variant Type

SNV

Location

8:10607375-10607375

Exon Numbers

4/4

Ref

T

Alt

C

Frequency (Read)

1.0 (870/870)

Zygosity

Homozygous

Uncontrolled when printed

59/79

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posi_con

Amino Acid Change (HGVSp)

NP_849188.4:p.Ser2241=

User Classification

BenignACMG Classification

BenignACMG Labels

BA1(gnomAD),BS1(gnomAD),BS3(ClinVar),BP7(VEP,dbscSNV,GERP)

Inheritance Pattern

Recessive, DominantVariant Functionsynonymous_variant

Allele frequency in gnomAD - whole
population

0.6191Allele frequency in gnomAD - East Asian

0.97771000 Genomes Minor Allele

C

1000 Genomes Minor Allele Frequency

0.651

SIFT Prediction-

dbSNP ID

rs56382513

ClinVar ID

361212ClinVar Pathogenicity

BenignHGMD-

GEM-J WGA Allele Frequency

0.916

Report Inclusion

None

Variant (HGVSc)

NM_178857.6:c.6418G>A

Gene Symbol

RP1L1

Variant Type

SNV

Location

8:10607680-10607680

Exon Numbers

4/4

Ref

C

Alt

T

Frequency (Read)

0.44262 (378/854)

Zygosity

Heterozygous

Amino Acid Change (HGVSp)

NP_849188.4:p.Glu2140Lys

User Classification

BenignACMG Classification

BenignACMG Labels

PP3(SIFT),BA1(gnomAD),BS1(gnomAD),BS3(ClinVar),BP1(ClinVar),BP4(BLOSUM)

Inheritance Pattern

Recessive, DominantVariant Function

missense_variant

Allele frequency in gnomAD - whole
population

0.138

Allele frequency in gnomAD - East Asian

0.4131000 Genomes Minor Allele

T1000 Genomes Minor Allele Frequency

0.1699SIFT Predictiondeleterious_low_confidence

dbSNP ID

rs72494282

ClinVar ID

361223

ClinVar Pathogenicity

BenignHGMD-

GEM-J WGA Allele Frequency

0.335

Report Inclusion

None

Variant (HGVSc)

NM_178857.6:c.6264G>T

Gene Symbol

RP1L1

Variant Type

SNV

Location

8:10607834-10607834

Exon Numbers

4/4

Ref

C

Alt

A

Frequency (Read)

0.45199 (386/854)

Zygosity

Heterozygous

Amino Acid Change (HGVSp)

NP_849188.4:p.Gln2088His

User Classification

BenignACMG Classification

BenignACMG Labels

BA1(gnomAD),BS1(gnomAD),BS3(ClinVar),BP1(ClinVar),BP4(SIFT),BP6(Benign Variants from PMID:31213501)

Inheritance Pattern

Recessive, DominantVariant Function

missense_variant

Allele frequency in gnomAD - whole
population

0.1317

Allele frequency in gnomAD - East Asian

0.3951000 Genomes Minor Allele

A

1000 Genomes Minor Allele Frequency

0.1641

SIFT Prediction

tolerated_low_confidence

dbSNP ID

rs11778341

ClinVar ID

361228

ClinVar Pathogenicity

BenignHGMD-

GEM-J WGA Allele Frequency

0.338

Report Inclusion

None

Uncontrolled when printed

60/79

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160

161

posi_con

Variant (HGVSc)

NM_178857.6:c.6209A>T

Gene Symbol

RP1L1

Variant Type

SNV

Location

8:10607889-10607889

Exon Numbers

4/4

Ref

T

Alt

A

Frequency (Read)

0.45574 (381/836)

Zygosity

Heterozygous

Amino Acid Change (HGVSp)

NP_849188.4:p.Glu2070Val

User Classification

BenignACMG Classification

BenignACMG Labels

PP3(BLOSUM),BA1(gnomAD),BS1(gnomAD),BS3(ClinVar),BP1(ClinVar),BP4(SIFT),BP6(Benign Variants from PMID:31213501)

Inheritance Pattern

Recessive, DominantVariant Function

missense_variant

Allele frequency in gnomAD - whole
population

0.1314

Allele frequency in gnomAD - East Asian

0.40291000 Genomes Minor Allele

A

1000 Genomes Minor Allele Frequency

0.1613

SIFT Prediction

tolerated_low_confidence

dbSNP ID

rs11782670

ClinVar ID

361229ClinVar Pathogenicity

BenignHGMD-

GEM-J WGA Allele Frequency

0.363

Report Inclusion

None

Variant (HGVSc)

NM_178857.6:c.5860A>G

Gene Symbol

RP1L1

Variant Type

SNV

Location

8:10608238-10608238

Exon Numbers

4/4

Ref

T

Alt

C

Frequency (Read)

1.0 (799/799)

Zygosity

Homozygous

Amino Acid Change (HGVSp)

NP_849188.4:p.Thr1954Ala

User Classification

BenignACMG Classification

BenignACMG Labels

BA1(gnomAD),BS1(gnomAD),BS3(ClinVar),BP1(ClinVar),BP4(SIFT),BP6(Benign Variants from PMID:31213501)

Inheritance Pattern

Recessive, DominantVariant Function

missense_variant

Allele frequency in gnomAD - whole
population

0.614

Allele frequency in gnomAD - East Asian

0.97781000 Genomes Minor Allele

C

1000 Genomes Minor Allele Frequency

0.6494

SIFT Prediction

tolerated_low_confidence

dbSNP ID

rs11783478

ClinVar ID

361235

ClinVar Pathogenicity

BenignHGMD-

GEM-J WGA Allele Frequency

0.918

Report Inclusion

None

Variant (HGVSc)

NM_178857.6:c.5666A>T

Gene Symbol

RP1L1

Variant Type

SNV

Location

8:10608432-10608432

Exon Numbers

4/4

Ref

T

Alt

A

Frequency (Read)

0.46002 (374/813)

Zygosity

Heterozygous

Amino Acid Change (HGVSp)

NP_849188.4:p.Asp1889Val

User Classification

BenignACMG Classification

BenignACMG Labels

PP3(BLOSUM),BA1(gnomAD),BS1(gnomAD),BS3(ClinVar),BP1(ClinVar),BP4(SIFT),BP6(Benign Variants from PMID:31213501)

Inheritance Pattern

Recessive, DominantVariant Function

missense_variant

Allele frequency in gnomAD - whole
population

0.2591Allele frequency in gnomAD - East Asian

0.4091

Uncontrolled when printed

61/79

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164

posi_con1000 Genomes Minor Allele

A

1000 Genomes Minor Allele Frequency

0.2374

SIFT Prediction

tolerated

dbSNP ID

rs28446662

ClinVar ID

361242ClinVar Pathogenicity

BenignHGMD-

GEM-J WGA Allele Frequency

0.37

Report Inclusion

None

Variant (HGVSc)

NM_178857.6:c.5126C>T

Gene Symbol

RP1L1

Variant Type

SNV

Location

8:10608972-10608972

Exon Numbers

4/4

Ref

G

Alt

A

Frequency (Read)

0.52658 (515/978)

Zygosity

Heterozygous

Amino Acid Change (HGVSp)

NP_849188.4:p.Ala1709Val

User Classification

BenignACMG Classification

BenignACMG Labels

BA1(gnomAD),BS1(gnomAD),BP1(ClinVar),BP4(SIFT),BP6(Benign Variants from PMID:31213501,ClinVar)

Inheritance Pattern

Recessive, DominantVariant Function

missense_variant

Allele frequency in gnomAD - whole
population

0.3744

Allele frequency in gnomAD - East Asian

0.02192

1000 Genomes Minor Allele

A

1000 Genomes Minor Allele Frequency

0.3107

SIFT Prediction

tolerated

dbSNP ID

rs13267180

ClinVar ID

361259ClinVar Pathogenicity

BenignHGMD-

GEM-J WGA Allele Frequency

0.084

Report Inclusion

None

Variant (HGVSc)

NM_178857.6:c.4484C>G

Gene Symbol

RP1L1

Variant Type

SNV

Location

8:10609614-10609614

Exon Numbers

4/4

Ref

G

Alt

C

Frequency (Read)

0.51653 (453/877)

Zygosity

Heterozygous

Amino Acid Change (HGVSp)

NP_849188.4:p.Pro1495Arg

User Classification

BenignACMG Classification

BenignACMG Labels

PP3(BLOSUM),BA1(gnomAD),BS1(gnomAD),BS3(ClinVar),BP1(ClinVar),BP4(SIFT),BP6(Benign Variants from PMID:31213501)

Inheritance Pattern

Recessive, DominantVariant Function

missense_variant

Allele frequency in gnomAD - whole
population

0.2983

Allele frequency in gnomAD - East Asian

0.4171000 Genomes Minor Allele

C

1000 Genomes Minor Allele Frequency

0.2817

SIFT Prediction

tolerated

dbSNP ID

rs4841399

ClinVar ID

361276

ClinVar Pathogenicity

BenignHGMD-

GEM-J WGA Allele Frequency

0.373

Report Inclusion

None

Variant (HGVSc)

NM_178857.6:c.4401G>T

Gene Symbol

RP1L1

Variant Type

SNV

Location

8:10609697-10609697

Exon Numbers

4/4

Ref

C

Alt

A

Frequency (Read)

0.99775 (888/890)

Zygosity

Homozygous

Uncontrolled when printed

62/79

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posi_con

Amino Acid Change (HGVSp)

NP_849188.4:p.Arg1467Ser

User Classification

BenignACMG Classification

BenignACMG Labels

PP3(BLOSUM),BA1(gnomAD),BS1(gnomAD),BS3(ClinVar),BP1(ClinVar),BP4(SIFT)

Inheritance Pattern

Recessive, DominantVariant Function

missense_variant

Allele frequency in gnomAD - whole
population

0.9842

Allele frequency in gnomAD - East Asian

0.99991000 Genomes Minor Allele

A

1000 Genomes Minor Allele Frequency

0.9409SIFT Prediction

tolerated

dbSNP ID

rs4840498

ClinVar ID

361282ClinVar Pathogenicity

BenignHGMD-

GEM-J WGA Allele Frequency

1.0

Report Inclusion

None

Variant (HGVSc)

NM_178857.6:c.4032A>G

Gene Symbol

RP1L1

Variant Type

SNV

Location

8:10610066-10610066

Exon Numbers

4/4

Ref

T

Alt

C

Frequency (Read)

0.43601 (293/672)

Zygosity

Heterozygous

Amino Acid Change (HGVSp)

NP_849188.4:p.Thr1344=

User Classification

BenignACMG Classification

BenignACMG Labels

BA1(gnomAD),BS1(gnomAD),BS3(ClinVar),BP7(VEP,dbscSNV,GERP)

Inheritance Pattern

Recessive, DominantVariant Functionsynonymous_variant

Allele frequency in gnomAD - whole
population

0.3331Allele frequency in gnomAD - East Asian

0.66621000 Genomes Minor Allele-

1000 Genomes Minor Allele Frequency-

SIFT Prediction-

dbSNP ID

rs4840499

ClinVar ID

361288

ClinVar Pathogenicity

BenignHGMD-

GEM-J WGA Allele Frequency

0.591

Report Inclusion

None

Variant (HGVSc)

NM_178857.6:c.3436C>T

Gene Symbol

RP1L1

Variant Type

SNV

Location

8:10610662-10610662

Exon Numbers

4/4

Ref

G

Alt

A

Frequency (Read)

1.0 (850/850)

Zygosity

Homozygous

Amino Acid Change (HGVSp)

NP_849188.4:p.Arg1146Trp

User Classification

BenignACMG Classification

BenignACMG Labels

PP3(SIFT),BA1(gnomAD),BS1(gnomAD),BS3(ClinVar),BP1(ClinVar),BP6(Benign Variants from PMID:31213501)

Inheritance Pattern

Recessive, DominantVariant Function

missense_variant

Allele frequency in gnomAD - whole
population

0.7332

Allele frequency in gnomAD - East Asian

0.62611000 Genomes Minor Allele

A

1000 Genomes Minor Allele Frequency

0.7081

SIFT Predictiondeleterious

dbSNP ID

rs4840502

ClinVar ID

361309ClinVar Pathogenicity

BenignHGMD-

GEM-J WGA Allele Frequency

0.63

Report Inclusion

None

Uncontrolled when printed

63/79

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168

169

posi_con

Variant (HGVSc)

NM_178857.6:c.2375T>C

Gene Symbol

RP1L1

Variant Type

SNV

Location

8:10611723-10611723

Exon Numbers

4/4

Ref

A

Alt

G

Frequency (Read)

0.52149 (449/861)

Zygosity

Heterozygous

Amino Acid Change (HGVSp)

NP_849188.4:p.Leu792Pro

User Classification

BenignACMG Classification

BenignACMG Labels

PP3(BLOSUM),BA1(gnomAD),BS1(gnomAD),BS3(ClinVar),BP1(ClinVar),BP4(SIFT),BP6(Benign Variants from PMID:31213501)

Inheritance Pattern

Recessive, DominantVariant Function

missense_variant

Allele frequency in gnomAD - whole
population

0.416

Allele frequency in gnomAD - East Asian

0.02226

1000 Genomes Minor Allele

G

1000 Genomes Minor Allele Frequency

0.3149SIFT Prediction

tolerated

dbSNP ID

rs35602868

ClinVar ID

361349ClinVar Pathogenicity

BenignHGMD-

GEM-J WGA Allele Frequency

0.084

Report Inclusion

None

Variant (HGVSc)

NM_178857.6:c.2316G>A

Gene Symbol

RP1L1

Variant Type

SNV

Location

8:10611782-10611782

Exon Numbers

4/4

Ref

C

Alt

T

Frequency (Read)

0.47843 (377/788)

Zygosity

Heterozygous

Amino Acid Change (HGVSp)

NP_849188.4:p.Ser772=

User Classification

BenignACMG Classification

BenignACMG Labels

BA1(gnomAD),BS1(gnomAD),BP6(ClinVar),BP7(VEP,dbscSNV,GERP)

Inheritance Pattern

Recessive, DominantVariant Functionsynonymous_variant

Allele frequency in gnomAD - whole
population

0.06764

Allele frequency in gnomAD - East Asian

1.67E-4

1000 Genomes Minor Allele

T1000 Genomes Minor Allele Frequency

0.0303

SIFT Prediction-

dbSNP ID

rs62490857

ClinVar ID

361352ClinVar Pathogenicity

BenignHGMD-

GEM-J WGA Allele Frequency-

Report Inclusion

None

Variant (HGVSc)

NM_178857.6:c.1791C>T

Gene Symbol

RP1L1

Variant Type

SNV

Location

8:10612307-10612307

Exon Numbers

4/4

Ref

G

Alt

A

Frequency (Read)

0.49143 (459/934)

Zygosity

Heterozygous

Amino Acid Change (HGVSp)

NP_849188.4:p.Gly597=

User Classification

BenignACMG Classification

BenignACMG Labels

BA1(gnomAD),BS1(gnomAD),BS3(ClinVar),BP7(VEP,dbscSNV,GERP)

Inheritance Pattern

Recessive, DominantVariant Functionsynonymous_variant

Allele frequency in gnomAD - whole
population

0.8441Allele frequency in gnomAD - East Asian

0.636

Uncontrolled when printed

64/79

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172

posi_con1000 Genomes Minor Allele

A

1000 Genomes Minor Allele Frequency

0.7973

SIFT Prediction-

dbSNP ID

rs6996950

ClinVar ID

361367

ClinVar Pathogenicity

BenignHGMD-

GEM-J WGA Allele Frequency

0.635

Report Inclusion

None

Variant (HGVSc)

NM_178857.6:c.665A>C

Gene Symbol

RP1L1

Variant Type

SNV

Location

8:10616532-10616532

Exon Numbers

3/4

Ref

T

Alt

G

Frequency (Read)

0.50809 (408/803)

Zygosity

Heterozygous

Amino Acid Change (HGVSp)

NP_849188.4:p.His222Pro

User Classification

BenignACMG Classification

BenignACMG Labels

PP3(SIFT),BA1(gnomAD),BS1(gnomAD),BS3(ClinVar),BP1(ClinVar),BP6(Benign Variants from PMID:31213501)

Inheritance Pattern

Recessive, DominantVariant Function

missense_variant

Allele frequency in gnomAD - whole
population

0.1861Allele frequency in gnomAD - East Asian

0.44431000 Genomes Minor Allele

G

1000 Genomes Minor Allele Frequency

0.2167

SIFT Predictiondeleterious

dbSNP ID

rs4388421

ClinVar ID

361399ClinVar Pathogenicity

BenignHGMD-

GEM-J WGA Allele Frequency

0.515

Report Inclusion

None

Variant (HGVSc)

NM_203288.2:c.314-9C>T

Gene Symbol

RP9Variant Type

SNV

Location

7:33097371-33097371

Exon Numbers

Intronic

Ref

G

Alt

A

Frequency (Read)

1.0 (388/388)

Zygosity

Homozygous

Amino Acid Change (HGVSp)-

User Classification

BenignACMG Classification

BenignACMG Labels

BA1(gnomAD),BS1(gnomAD),BS3(ClinVar)

Inheritance Pattern

Dominant

Variant Function

splice_polypyrimidine_tract_variant,intron_variant

Allele frequency in gnomAD - whole
population

0.9936

Allele frequency in gnomAD - East Asian

0.99931000 Genomes Minor Allele

A

1000 Genomes Minor Allele Frequency

0.9966

SIFT Prediction-

dbSNP ID

rs6462460

ClinVar ID

360045

ClinVar Pathogenicity

BenignHGMD-

GEM-J WGA Allele Frequency

1.0

Report Inclusion

None

Variant (HGVSc)

NM_020366.4:c.287C>A

Gene Symbol

RPGRIP1

Variant Type

SNV

Location

14:21301034-21301034

Exon Numbers

4/25

Ref

C

Alt

A

Frequency (Read)

0.49773 (439/882)

Zygosity

Heterozygous

Uncontrolled when printed

65/79

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174

posi_con

Amino Acid Change (HGVSp)

NP_065099.3:p.Pro96Gln

User Classification

BenignACMG Classification

BenignACMG Labels

PP3(BLOSUM),BA1(gnomAD),BS1(gnomAD),BS3(ClinVar),BP1(ClinVar),BP4(SIFT)

Inheritance Pattern

Recessive

Variant Function

missense_variant

Allele frequency in gnomAD - whole
population

0.07088

Allele frequency in gnomAD - East Asian

0.03546

1000 Genomes Minor Allele

A

1000 Genomes Minor Allele Frequency

0.0583

SIFT Prediction

tolerated

dbSNP ID

rs1040904

ClinVar ID

99819

ClinVar Pathogenicity

BenignHGMD-

GEM-J WGA Allele Frequency

0.024

Report Inclusion

None

Variant (HGVSc)

NM_020366.4:c.574A>G

Gene Symbol

RPGRIP1

Variant Type

SNV

Location

14:21302571-21302571

Exon Numbers

5/25

Ref

A

Alt

G

Frequency (Read)

1.0 (614/614)

Zygosity

Homozygous

Amino Acid Change (HGVSp)

NP_065099.3:p.Lys192Glu

User Classification

BenignACMG Classification

BenignACMG Labels

BA1(gnomAD),BS1(gnomAD),BS3(ClinVar),BP1(ClinVar),BP4(SIFT)

Inheritance Pattern

Recessive

Variant Function

missense_variant

Allele frequency in gnomAD - whole
population

0.5032

Allele frequency in gnomAD - East Asian

0.32671000 Genomes Minor Allele

G

1000 Genomes Minor Allele Frequency

0.4772SIFT Prediction

tolerated

dbSNP ID

rs6571751

ClinVar ID

99827

ClinVar Pathogenicity

BenignHGMD-

GEM-J WGA Allele Frequency

0.292

Report Inclusion

None

Variant (HGVSc)

NM_000541.5:c.1207G>A

Gene Symbol

SAG

Variant Type

SNV

Location

2:233346901-233346901

Exon Numbers

16/16

Ref

G

Alt

A

Frequency (Read)

1.0 (597/597)

Zygosity

Homozygous

Amino Acid Change (HGVSp)

NP_000532.2:p.Val403Ile

User Classification

BenignACMG Classification

BenignACMG Labels

BA1(gnomAD),BS1(gnomAD),BS3(ClinVar),BP1(ClinVar),BP4(SIFT),BP6(Benign Variants from PMID:31213501)

Inheritance Pattern

Recessive, DominantVariant Function

missense_variant

Allele frequency in gnomAD - whole
population

0.3669Allele frequency in gnomAD - East Asian

0.41221000 Genomes Minor Allele

A

1000 Genomes Minor Allele Frequency

0.3029SIFT Prediction

tolerated_low_confidence

dbSNP ID

rs1046974

ClinVar ID

194606

ClinVar Pathogenicity

BenignHGMD-

GEM-J WGA Allele Frequency

0.295

Report Inclusion

None

Uncontrolled when printed

66/79

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177

posi_con

Variant (HGVSc)

NM_014014.5:c.3550T>C

Gene Symbol

SNRNP200

Variant Type

SNV

Location

2:96287095-96287095

Exon Numbers

27/45

Ref

A

Alt

G

Frequency (Read)

0.50126 (399/796)

Zygosity

Heterozygous

Amino Acid Change (HGVSp)

NP_054733.2:p.Leu1184=

User Classification

BenignACMG Classification

BenignACMG Labels

BA1(gnomAD),BS1(gnomAD),BS3(ClinVar),BP7(VEP,dbscSNV,GERP)

Inheritance Pattern

Dominant

Variant Functionsynonymous_variant

Allele frequency in gnomAD - whole
population

0.3152

Allele frequency in gnomAD - East Asian

0.17681000 Genomes Minor Allele

G

1000 Genomes Minor Allele Frequency

0.2841

SIFT Prediction-

dbSNP ID

rs3171927

ClinVar ID

337548

ClinVar Pathogenicity

BenignHGMD-

GEM-J WGA Allele Frequency

0.279

Report Inclusion

None

Variant (HGVSc)

NM_018418.5:c.220G>A

Gene Symbol

SPATA7

Variant Type

SNV

Location

14:88396185-88396185

Exon Numbers

4/12

Ref

G

Alt

A

Frequency (Read)

0.39338 (107/272)

Zygosity

Heterozygous

Amino Acid Change (HGVSp)

NP_060888.2:p.Val74Met

User Classification

BenignACMG Classification

BenignACMG Labels

BA1(gnomAD),BS1(gnomAD),BS3(ClinVar),BP1(ClinVar),BP4(SIFT),BP6(Benign Variants from PMID:31213501)

Inheritance Pattern

Recessive

Variant Function

missense_variant

Allele frequency in gnomAD - whole
population

0.3368Allele frequency in gnomAD - East Asian

0.31981000 Genomes Minor Allele

A

1000 Genomes Minor Allele Frequency

0.4075

SIFT Prediction

tolerated

dbSNP ID

rs3179969

ClinVar ID

286866

ClinVar Pathogenicity

BenignHGMD-

GEM-J WGA Allele Frequency

0.285

Report Inclusion

None

Variant (HGVSc)

NM_005802.5:c.2319T>C

Gene Symbol

TOPORS

Variant Type

SNV

Location

9:32542206-32542206

Exon Numbers

3/3

Ref

A

Alt

G

Frequency (Read)

0.47067 (337/716)

Zygosity

Heterozygous

Amino Acid Change (HGVSp)

NP_005793.2:p.Ser773=

User Classification

BenignACMG Classification

BenignACMG Labels

BA1(gnomAD),BS1(gnomAD),BS3(ClinVar),BP7(VEP,dbscSNV,GERP)

Inheritance Pattern

Dominant

Variant Functionsynonymous_variant

Allele frequency in gnomAD - whole
population

0.2085Allele frequency in gnomAD - East Asian

0.07645

Uncontrolled when printed

67/79

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180

posi_con1000 Genomes Minor Allele

G

1000 Genomes Minor Allele Frequency

0.1791

SIFT Prediction-

dbSNP ID

rs10971019

ClinVar ID

95313

ClinVar Pathogenicity

BenignHGMD-

GEM-J WGA Allele Frequency

0.085

Report Inclusion

None

Variant (HGVSc)

NM_003322.6:c.783G>C

Gene Symbol

TULP1

Variant Type

SNV

Location

6:35509248-35509248

Exon Numbers

8/15

Ref

C

Alt

G

Frequency (Read)

0.5221 (378/724)

Zygosity

Heterozygous

Amino Acid Change (HGVSp)

NP_003313.3:p.Lys261Asn

User Classification

BenignACMG Classification

BenignACMG Labels

BA1(gnomAD),BS1(gnomAD),BS3(ClinVar),BP4(SIFT),BP6(Benign Variants from PMID:31213501)

Inheritance Pattern

Recessive

Variant Function

missense_variant

Allele frequency in gnomAD - whole
population

0.8228Allele frequency in gnomAD - East Asian

0.84041000 Genomes Minor Allele

G

1000 Genomes Minor Allele Frequency

0.8385

SIFT Prediction

tolerated

dbSNP ID

rs2064318

ClinVar ID

94127

ClinVar Pathogenicity

BenignHGMD-

GEM-J WGA Allele Frequency

0.864

Report Inclusion

None

Variant (HGVSc)

NM_003322.6:c.776T>C

Gene Symbol

TULP1

Variant Type

SNV

Location

6:35509255-35509255

Exon Numbers

8/15

Ref

A

Alt

G

Frequency (Read)

0.51582 (375/727)

Zygosity

Heterozygous

Amino Acid Change (HGVSp)

NP_003313.3:p.Ile259Thr

User Classification

BenignACMG Classification

BenignACMG Labels

PP3(BLOSUM),BA1(gnomAD),BS1(gnomAD),BS3(ClinVar),BP4(SIFT),BP6(Benign Variants from PMID:31213501)

Inheritance Pattern

Recessive

Variant Function

missense_variant

Allele frequency in gnomAD - whole
population

0.3811Allele frequency in gnomAD - East Asian

0.4931000 Genomes Minor Allele

G

1000 Genomes Minor Allele Frequency

0.394

SIFT Prediction

tolerated

dbSNP ID

rs2064317

ClinVar ID

99671

ClinVar Pathogenicity

BenignHGMD-

GEM-J WGA Allele Frequency

0.392

Report Inclusion

None

Variant (HGVSc)

NM_003322.6:c.200C>G

Gene Symbol

TULP1

Variant Type

SNV

Location

6:35511797-35511797

Exon Numbers

4/15

Ref

G

Alt

C

Frequency (Read)

0.49074 (371/756)

Zygosity

Heterozygous

Uncontrolled when printed

68/79

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182

posi_con

Amino Acid Change (HGVSp)

NP_003313.3:p.Thr67Arg

User Classification

BenignACMG Classification

BenignACMG Labels

PP3(BLOSUM),BA1(gnomAD),BS1(gnomAD),BS3(ClinVar),BP4(SIFT),BP6(Benign Variants from PMID:31213501)

Inheritance Pattern

Recessive

Variant Function

missense_variant

Allele frequency in gnomAD - whole
population

0.851

Allele frequency in gnomAD - East Asian

0.84281000 Genomes Minor Allele

C

1000 Genomes Minor Allele Frequency

0.8744

SIFT Prediction

tolerated_low_confidence

dbSNP ID

rs7764472

ClinVar ID

286865

ClinVar Pathogenicity

BenignHGMD-

GEM-J WGA Allele Frequency

0.865

Report Inclusion

None

Variant (HGVSc)

NM_206933.4:c.13297G>T

Gene Symbol

USH2A

Variant Type

SNV

Location

1:215674614-215674614

Exon Numbers

63/72

Ref

C

Alt

A

Frequency (Read)

0.54096 (350/647)

Zygosity

Heterozygous

Amino Acid Change (HGVSp)

NP_996816.3:p.Val4433Leu

User Classification

BenignACMG Classification

BenignACMG Labels

BS1(gnomAD),BS3(ClinVar),BP1(ClinVar),BP4(SIFT)

Inheritance Pattern

Recessive

Variant Function

missense_variant

Allele frequency in gnomAD - whole
population

0.01914

Allele frequency in gnomAD - East Asian

0.01000 Genomes Minor Allele

A

1000 Genomes Minor Allele Frequency

0.005

SIFT Prediction

tolerated

dbSNP ID

rs111033381

ClinVar ID

48415

ClinVar Pathogenicity

BenignHGMD-

GEM-J WGA Allele Frequency-

Report Inclusion

None

Variant (HGVSc)

NM_206933.4:c.13191G>A

Gene Symbol

USH2A

Variant Type

SNV

Location

1:215674720-215674720

Exon Numbers

63/72

Ref

C

Alt

T

Frequency (Read)

0.45203 (245/542)

Zygosity

Heterozygous

Amino Acid Change (HGVSp)

NP_996816.3:p.Glu4397=

User Classification

BenignACMG Classification

BenignACMG Labels

BA1(gnomAD),BS1(gnomAD),BS3(ClinVar),BP7(VEP,dbscSNV,GERP)

Inheritance Pattern

Recessive

Variant Functionsynonymous_variant

Allele frequency in gnomAD - whole
population

0.2029Allele frequency in gnomAD - East Asian

0.35221000 Genomes Minor Allele

T1000 Genomes Minor Allele Frequency

0.2035

SIFT Prediction-

dbSNP ID

rs2009923

ClinVar ID

48413

ClinVar Pathogenicity

BenignHGMD-

GEM-J WGA Allele Frequency

0.382

Report Inclusion

None

Uncontrolled when printed

69/79

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184

185

posi_con

Variant (HGVSc)

NM_206933.4:c.12612A>G

Gene Symbol

USH2A

Variant Type

SNV

Location

1:215675299-215675299

Exon Numbers

63/72

Ref

T

Alt

C

Frequency (Read)

0.51903 (300/578)

Zygosity

Heterozygous

Amino Acid Change (HGVSp)

NP_996816.3:p.Thr4204=

User Classification

BenignACMG Classification

BenignACMG Labels

BA1(gnomAD),BS1(gnomAD),BS3(ClinVar),BP7(VEP,dbscSNV,GERP)

Inheritance Pattern

Recessive

Variant Functionsynonymous_variant

Allele frequency in gnomAD - whole
population

0.7669Allele frequency in gnomAD - East Asian

0.64741000 Genomes Minor Allele

C

1000 Genomes Minor Allele Frequency

0.6897

SIFT Prediction-

dbSNP ID

rs2797235

ClinVar ID

177993

ClinVar Pathogenicity

BenignHGMD-

GEM-J WGA Allele Frequency

0.613

Report Inclusion

None

Variant (HGVSc)

NM_206933.4:c.10232A>C

Gene Symbol

USH2A

Variant Type

SNV

Location

1:215786825-215786825

Exon Numbers

52/72

Ref

T

Alt

G

Frequency (Read)

0.52161 (362/694)

Zygosity

Heterozygous

Amino Acid Change (HGVSp)

NP_996816.3:p.Glu3411Ala

User Classification

BenignACMG Classification

BenignACMG Labels

PP3(BLOSUM),BA1(gnomAD),BS1(gnomAD),BS3(ClinVar),BP1(ClinVar),BP4(SIFT),BP6(Benign Variants from PMID:31213501)

Inheritance Pattern

Recessive

Variant Function

missense_variant

Allele frequency in gnomAD - whole
population

0.5482

Allele frequency in gnomAD - East Asian

0.63421000 Genomes Minor Allele

G

1000 Genomes Minor Allele Frequency

0.5887

SIFT Prediction

tolerated

dbSNP ID

rs10864198

ClinVar ID

48344

ClinVar Pathogenicity

BenignHGMD-

GEM-J WGA Allele Frequency

0.619

Report Inclusion

None

Variant (HGVSc)

NM_206933.4:c.6506T>C

Gene Symbol

USH2A

Variant Type

SNV

Location

1:215999038-215999038

Exon Numbers

34/72

Ref

A

Alt

G

Frequency (Read)

0.50519 (146/289)

Zygosity

Heterozygous

Amino Acid Change (HGVSp)

NP_996816.3:p.Ile2169Thr

User Classification

BenignACMG Classification

BenignACMG Labels

PP3(BLOSUM),BA1(gnomAD),BS1(gnomAD),BS3(ClinVar),BP1(ClinVar),BP4(SIFT),BP6(Benign Variants from PMID:31213501)

Inheritance Pattern

Recessive

Variant Function

missense_variant

Allele frequency in gnomAD - whole
population

0.5628Allele frequency in gnomAD - East Asian

0.8405

Uncontrolled when printed

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188

posi_con1000 Genomes Minor Allele

G

1000 Genomes Minor Allele Frequency

0.5935

SIFT Prediction

tolerated

dbSNP ID

rs10864219

ClinVar ID

48562

ClinVar Pathogenicity

BenignHGMD-

GEM-J WGA Allele Frequency

0.886

Report Inclusion

None

Variant (HGVSc)

NM_206933.4:c.6317T>C

Gene Symbol

USH2A

Variant Type

SNV

Location

1:216046439-216046439

Exon Numbers

32/72

Ref

A

Alt

G

Frequency (Read)

0.52826 (243/460)

Zygosity

Heterozygous

Amino Acid Change (HGVSp)

NP_996816.3:p.Ile2106Thr

User Classification

BenignACMG Classification

BenignACMG Labels

PP3(BLOSUM),BA1(gnomAD),BS1(gnomAD),BS3(ClinVar),BP1(ClinVar),BP4(SIFT),BP6(Benign Variants from PMID:31213501)

Inheritance Pattern

Recessive

Variant Function

missense_variant

Allele frequency in gnomAD - whole
population

0.5943

Allele frequency in gnomAD - East Asian

0.44081000 Genomes Minor Allele

G

1000 Genomes Minor Allele Frequency

0.5956

SIFT Prediction

tolerated

dbSNP ID

rs6657250

ClinVar ID

167815

ClinVar Pathogenicity

BenignHGMD-

GEM-J WGA Allele Frequency

0.441

Report Inclusion

None

Variant (HGVSc)

NM_206933.4:c.4994T>C

Gene Symbol

USH2A

Variant Type

SNV

Location

1:216084871-216084871

Exon Numbers

25/72

Ref

A

Alt

G

Frequency (Read)

0.52159 (157/301)

Zygosity

Heterozygous

Amino Acid Change (HGVSp)

NP_996816.3:p.Ile1665Thr

User Classification

BenignACMG Classification

BenignACMG Labels

PP3(BLOSUM),BA1(gnomAD),BS1(gnomAD),BS3(ClinVar),BP1(ClinVar),BP4(SIFT),BP6(Benign Variants from PMID:31213501)

Inheritance Pattern

Recessive

Variant Function

missense_variant

Allele frequency in gnomAD - whole
population

0.1104

Allele frequency in gnomAD - East Asian

0.02091000 Genomes Minor Allele

G

1000 Genomes Minor Allele Frequency

0.0627

SIFT Prediction

tolerated

dbSNP ID

rs56222536

ClinVar ID

48525

ClinVar Pathogenicity

BenignHGMD-

GEM-J WGA Allele Frequency

0.019

Report Inclusion

None

Variant (HGVSc)

NM_206933.4:c.4457G>A

Gene Symbol

USH2A

Variant Type

SNV

Location

1:216175422-216175422

Exon Numbers

21/72

Ref

C

Alt

T

Frequency (Read)

0.51211 (296/578)

Zygosity

Heterozygous

Uncontrolled when printed

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posi_con

Amino Acid Change (HGVSp)

NP_996816.3:p.Arg1486Lys

User Classification

BenignACMG Classification

BenignACMG Labels

BA1(gnomAD),BS1(gnomAD),BS3(ClinVar),BP1(ClinVar),BP4(SIFT),BP6(Benign Variants from PMID:31213501)

Inheritance Pattern

Recessive

Variant Function

missense_variant

Allele frequency in gnomAD - whole
population

0.6605Allele frequency in gnomAD - East Asian

0.78131000 Genomes Minor Allele

T1000 Genomes Minor Allele Frequency

0.6623

SIFT Prediction

tolerated

dbSNP ID

rs1805049

ClinVar ID

177992ClinVar Pathogenicity

BenignHGMD-

GEM-J WGA Allele Frequency

0.818

Report Inclusion

None

Variant (HGVSc)

NM_206933.4:c.2109T>C

Gene Symbol

USH2A

Variant Type

SNV

Location

1:216250961-216250961

Exon Numbers

12/72

Ref

A

Alt

G

Frequency (Read)

0.49721 (356/716)

Zygosity

Heterozygous

Amino Acid Change (HGVSp)

NP_996816.3:p.Asp703=

User Classification

BenignACMG Classification

BenignACMG Labels

BS1(gnomAD),BS3(ClinVar),BP7(VEP,dbscSNV,GERP)

Inheritance Pattern

Recessive

Variant Functionsynonymous_variant

Allele frequency in gnomAD - whole
population

0.01698

Allele frequency in gnomAD - East Asian

0.01000 Genomes Minor Allele

G

1000 Genomes Minor Allele Frequency

0.0074

SIFT Prediction-

dbSNP ID

rs45555435

ClinVar ID

48483

ClinVar Pathogenicity

Benign/Likely_benign

HGMD

-

GEM-J WGA Allele Frequency-

Report Inclusion

None

Variant (HGVSc)

NM_206933.4:c.1931A>T

Gene Symbol

USH2A

Variant Type

SNV

Location

1:216289320-216289320

Exon Numbers

11/72

Ref

T

Alt

A

Frequency (Read)

0.53846 (308/572)

Zygosity

Heterozygous

Amino Acid Change (HGVSp)

NP_996816.3:p.Asp644Val

User Classification

BenignACMG Classification

BenignACMG Labels

PP3(BLOSUM),BA1(gnomAD),BS1(gnomAD),BS3(ClinVar),BP1(ClinVar),BP4(SIFT)

Inheritance Pattern

Recessive

Variant Function

missense_variant

Allele frequency in gnomAD - whole
population

0.0581Allele frequency in gnomAD - East Asian

5.989E-4

1000 Genomes Minor Allele

A

1000 Genomes Minor Allele Frequency

0.0345

SIFT Prediction

tolerated

dbSNP ID

rs1805048

ClinVar ID

48478

ClinVar Pathogenicity

Benign/Likely_benign

HGMD

-

GEM-J WGA Allele Frequency-

Report Inclusion

None

Uncontrolled when printed

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Variant (HGVSc)

NM_206933.4:c.1419C>T

Gene Symbol

USH2A

Variant Type

SNV

Location

1:216323605-216323605

Exon Numbers

8/72

Ref

G

Alt

A

Frequency (Read)

0.46082 (247/536)

Zygosity

Heterozygous

Amino Acid Change (HGVSp)

NP_996816.3:p.Thr473=

User Classification

BenignACMG Classification

BenignACMG Labels

BA1(gnomAD),BS1(gnomAD),BS3(ClinVar),BP7(VEP,dbscSNV,GERP)

Inheritance Pattern

Recessive

Variant Functionsynonymous_variant

Allele frequency in gnomAD - whole
population

0.2499Allele frequency in gnomAD - East Asian

0.13371000 Genomes Minor Allele

A

1000 Genomes Minor Allele Frequency

0.263

SIFT Prediction-

dbSNP ID

rs1805050

ClinVar ID

48431

ClinVar Pathogenicity

BenignHGMD-

GEM-J WGA Allele Frequency

0.124

Report Inclusion

None

CNV Information (as Reference)
1

2

3

4

5

6

7

Variant (ISCN)

seq[GRCh38] 1q31.3(195134497_197328497)x1

Variant Type

Deletion

Location

1:195134497-197328497

Copy Number

1

Log Ratio-0.617

Genes

CRB1 (exons 1-2/12)

User Classification

Unclassified

Variant (ISCN)

seq[GRCh38] 2q13q13(111996876_111997026)x1

Variant Type

Deletion

Location

2:111996876-111997026

Copy Number

1

Log Ratio-1.055Genes

MERTK (intronic)

User Classification

Unclassified

Variant (ISCN)

seq[GRCh38] 4p15.32p15.32(15979817_15979967)x1

Variant Type

Deletion

Location

4:15979817-15979967

Copy Number

1

Log Ratio-1.425

Genes

PROM1 (exon 25/28)

User Classification

Unclassified

Variant (ISCN)

seq[GRCh38] 5q14.3q14.3(90724940_90725233)x1

Variant Type

Deletion

Location

5:90724940-90725233

Copy Number

1

Log Ratio-0.942Genes

ADGRV1 (exons 46-47/90)

User Classification

Unclassified

Variant (ISCN)

seq[GRCh38] 6q12q13(65553302_70093966)x1

Variant Type

Deletion

Location

6:65553302-70093966

Copy Number

1

Log Ratio-0.664Genes

EYS (exons 1-2/43), EYS (exons 1-2/44)

User Classification

Unclassified

Variant (ISCN)

seq[GRCh38] 8q21.3q21.3(86644578_86654111)x1

Variant Type

Deletion

Location

8:86644578-86654111

Copy Number

1

Log Ratio

-0.6

Genes

CNGB3 (exons 7-9/18)

User Classification

Unclassified

Variant (ISCN)

seq[GRCh38] 12q21.32q21.32(88087770_88087953)x1

Uncontrolled when printed

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posi_con

Variant Type

Deletion

Location

12:88087770-88087953

Copy Number

1

Log Ratio-0.835Genes

CEP290 (exon 32/54)

User Classification

Unclassified

Variant (ISCN)

seq[GRCh38] 14q31.3q31.3(88841394_88846711)x1

Variant Type

Deletion

Location

14:88841394-88846711

Copy Number

1

Log Ratio

-0.62

Genes

TTC8 (exons 6-7/15)

User Classification

Unclassified

Variant (ISCN)

seq[GRCh38] Xp11.4p11.4(38290916_38292816)x1

Variant Type

Deletion

Location

X:38290916-38292816

Copy Number

1

Log Ratio-0.663

Genes

RPGR (exons 12-13/19), RPGR (exons 12-13/15)

User Classification

Unclassified

Appendix 1: Disease Category Referred From RetNet
Gene

Associated Diseases

ABCA4

Cone or cone-rod dystrophy, autosomal recessive; Macular degeneration, autosomal recessive; Retinitis pigmentosa, autosomal recessive

ADGRV1

Usher syndrome, autosomal recessive

AIPL1

Cone or cone-rod dystrophy, autosomal dominant; Leber congenital amaurosis, autosomal recessive

BEST1

Macular degeneration, autosomal dominant; Retinitis pigmentosa, autosomal dominant; Retinitis pigmentosa, autosomal recessive; Other retinopathy, autosomal dominant; Other
retinopathy, autosomal recessive

C8orf37

Bardet-Biedl syndrome, autosomal recessive; Cone or cone-rod dystrophy, autosomal recessive; Retinitis pigmentosa, autosomal recessive

CA4

Retinitis pigmentosa, autosomal dominant

CACNA1F Cone or cone-rod dystrophy, X-linked; Congenital stationary night blindness, X-linked; Other retinopathy, X-linked
CDH23

Deafness alone or syndromic, autosomal recessive; Usher syndrome, autosomal recessive

CDHR1

Cone or cone-rod dystrophy, autosomal recessive

CEP290Bardet-Biedl syndrome, autosomal recessive; Leber congenital amaurosis, autosomal recessive; Syndromic/systemic diseases with retinopathy, autosomal recessive

CERKL

Cone or cone-rod dystrophy, autosomal recessive; Retinitis pigmentosa, autosomal recessive

CFAP410

Cone or cone-rod dystrophy, autosomal recessive

CHM

Other retinopathy, X-linked

CLRN1

Retinitis pigmentosa, autosomal recessive; Usher syndrome, autosomal recessive

CNGA1

Retinitis pigmentosa, autosomal recessive

CNGA3

Cone or cone-rod dystrophy, autosomal recessive; Other retinopathy, autosomal recessive

CNGB1

Retinitis pigmentosa, autosomal recessive

CNGB3

Cone or cone-rod dystrophy, autosomal recessive; Other retinopathy, autosomal recessive

CRB1

Leber congenital amaurosis, autosomal recessive; Retinitis pigmentosa, autosomal recessive; Other retinopathy, autosomal dominant

CRX

Cone or cone-rod dystrophy, autosomal dominant; Leber congenital amaurosis, autosomal dominant; Leber congenital amaurosis, autosomal recessive; Retinitis pigmentosa,
autosomal dominant

CYP4V2Retinitis pigmentosa, autosomal recessive; Other retinopathy, autosomal recessive

DHDDS

Retinitis pigmentosa, autosomal recessive

DRAM2

Macular degeneration, autosomal recessive

EYS

Retinitis pigmentosa, autosomal recessive

FAM161A

Retinitis pigmentosa, autosomal recessive

FSCN2

Macular degeneration, autosomal dominant; Retinitis pigmentosa, autosomal dominant

GNAT2

Cone or cone-rod dystrophy, autosomal recessive

GRK1

Congenital stationary night blindness, autosomal recessive

GUCA1A

Cone or cone-rod dystrophy, autosomal dominant

GUCA1B

Macular degeneration, autosomal dominant; Retinitis pigmentosa, autosomal dominant

GUCY2D

Cone or cone-rod dystrophy, autosomal dominant; Leber congenital amaurosis, autosomal recessive

IDH3B

Retinitis pigmentosa, autosomal recessive

IMPDH1

Leber congenital amaurosis, autosomal dominant; Retinitis pigmentosa, autosomal dominant

IMPG2Retinitis pigmentosa, autosomal recessive

IQCB1

Leber congenital amaurosis, autosomal recessive; Syndromic/systemic diseases with retinopathy, autosomal recessive

KCNV2

Cone or cone-rod dystrophy, autosomal recessive

KLHL7

Retinitis pigmentosa, autosomal dominant

LRAT

Leber congenital amaurosis, autosomal recessive; Retinitis pigmentosa, autosomal recessive

MAK

Retinitis pigmentosa, autosomal recessive

MERTK

Retinitis pigmentosa, autosomal recessive

MYO7A

Deafness alone or syndromic, autosomal recessive; Usher syndrome, autosomal recessive

NMNAT1

Leber congenital amaurosis, autosomal recessive

NR2E3

Retinitis pigmentosa, autosomal dominant; Retinitis pigmentosa, autosomal recessive; Other retinopathy, autosomal recessive

NRL

Retinitis pigmentosa, autosomal dominant; Retinitis pigmentosa, autosomal recessive

NYX

Congenital stationary night blindness, X-linked

PCARE

Retinitis pigmentosa, autosomal recessive

PDE6A

Retinitis pigmentosa, autosomal recessive

Uncontrolled when printed

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PDE6B

Congenital stationary night blindness, autosomal dominant; Retinitis pigmentosa, autosomal recessive

PDE6C

Cone or cone-rod dystrophy, autosomal recessive

PDE6G

Retinitis pigmentosa, autosomal recessive

POC1B

Cone or cone-rod dystrophy, autosomal recessive; Syndromic/systemic diseases with retinopathy, autosomal recessive

PRCD

Retinitis pigmentosa, autosomal recessive

PROM1

Cone or cone-rod dystrophy, autosomal dominant; Macular degeneration, autosomal dominant; Retinitis pigmentosa, autosomal recessive; Other retinopathy, autosomal recessive

PRPF3

Retinitis pigmentosa, autosomal dominant

PRPF31Retinitis pigmentosa, autosomal dominant

PRPF6

Retinitis pigmentosa, autosomal dominant

PRPF8Retinitis pigmentosa, autosomal dominant

PRPH2

Cone or cone-rod dystrophy, autosomal dominant; Leber congenital amaurosis, autosomal recessive; Macular degeneration, autosomal dominant; Retinitis pigmentosa, autosomal
dominant

RBP3

Retinitis pigmentosa, autosomal recessive

RDH12

Leber congenital amaurosis, autosomal recessive; Retinitis pigmentosa, autosomal dominant

RDH5

Cone or cone-rod dystrophy, autosomal recessive; Congenital stationary night blindness, autosomal recessive

RGR

Chorioretinal atrophy or degeneration, autosomal dominant; Retinitis pigmentosa, autosomal recessive

RGS9BP

Other retinopathy, autosomal recessive

RHO

Congenital stationary night blindness, autosomal dominant; Retinitis pigmentosa, autosomal dominant; Retinitis pigmentosa, autosomal recessive

RLBP1

Retinitis pigmentosa, autosomal recessive; Other retinopathy, autosomal recessive

ROM1

Retinitis pigmentosa, autosomal dominant

RP1

Retinitis pigmentosa, autosomal dominant; Retinitis pigmentosa, autosomal recessive

RP1L1

Macular degeneration, autosomal dominant; Retinitis pigmentosa, autosomal recessive

RP2

Retinitis pigmentosa, X-linked

RP9Retinitis pigmentosa, autosomal dominant

RPE65

Leber congenital amaurosis, autosomal recessive; Retinitis pigmentosa, autosomal dominant; Retinitis pigmentosa, autosomal recessive

RPGR

Cone or cone-rod dystrophy, X-linked; Macular degeneration, X-linked; Retinitis pigmentosa, X-linked

RPGRIP1

Cone or cone-rod dystrophy, autosomal recessive; Leber congenital amaurosis, autosomal recessive

RS1

Other retinopathy, X-linked

SAG

Congenital stationary night blindness, autosomal recessive; Retinitis pigmentosa, autosomal dominant; Retinitis pigmentosa, autosomal recessive

SEMA4A

Cone or cone-rod dystrophy, autosomal dominant; Retinitis pigmentosa, autosomal dominant

SNRNP200 Retinitis pigmentosa, autosomal dominant
SPATA7

Leber congenital amaurosis, autosomal recessive; Retinitis pigmentosa, autosomal recessive

TOPORS

Retinitis pigmentosa, autosomal dominant

TTC8

Bardet-Biedl syndrome, autosomal recessive; Retinitis pigmentosa, autosomal recessive

TULP1

Leber congenital amaurosis, autosomal recessive; Retinitis pigmentosa, autosomal recessive

USH2A

Retinitis pigmentosa, autosomal recessive; Usher syndrome, autosomal recessive

ZNF513Retinitis pigmentosa, autosomal recessive

Appendix 2: Criteria for classifying pathogenic and benign variants based on ACMG guidelines
Very strong evidence of pathogenicity
PVS1 Null variant (nonsense, frameshift, canonical ±1 or 2 splice sites, initiation codon) in a gene where loss of function (LOF) is a known mechanism of disease. SOURCE=VEP Impact
Strong evidence of pathogenicity
PS1

Same amino acid change as a previously established pathogenic variant regardless of nucleotide change. SOURCE=ClinVar, HGMD, Custom Variant List

PS3

Well-established in vitro or in vivo functional studies supportive of a damaging effect on the gene or gene product. SOURCE= ClinVar, HGMD

Moderate evidence of pathogenicity
PM1 Located in a mutational hot spot and/or critical and well-established functional domain without benign variation. SOURCE=ClinVar, PFAM
PM2 Absent from controls if dominant or with a frequency <= 0.5% if recessive in gnomAD database. SOURCE=gnomAD Allele Frequency
PM4 Protein length changes due to in-frame deletions/insertions in a non-repeat region or stop-loss variants. SOURCE=VEP consequence, Repeat Masker
PM5

Novel missense change at an amino acid residue where a different missense change determined to be pathogenic and has been seen before. SOURCE= ClinVar, HGMD, Custom Variant
List

Supporting evidence of pathogenicity
PP2

Missense variant in a gene that has a low rate of benign missense variation and where missense variants are a common mechanism of disease. SOURCE=ClinVar

PP3

Multiple lines of computational evidence support a deleterious effect on the gene or gene product (conservation, evolutionary, splicing impact, etc.). SOURCE= SIFT, BLOSUM62, dbscSNV,
GERP

PP5

Reputable source recently reports variant as pathogenic but the evidence is not available to the laboratory to perform an independent evaluation. SOURCE=ClinVar, HGMD, Pathogenic
Variants from PMID:31213501

Stand-Alone evidence of benign impact
BA1

Allele frequency is above 5% in gnomAD database. SOURCE=gnomAD Allele Frequency

Strong evidence of benign impact
BS1

Allele frequency is greater than 0.5% for disorder. SOURCE=gnomAD Allele Frequency

BS3

Well-established in vitro or in vivo functional studies show no damaging effect on protein function or splicing. SOURCE=ClinVar

Supporting evidence of benign impact
BP1

Missense variant in a gene for which primarily truncating variants are known to cause disease. SOURCE=ClinVar

BP3

In-frame deletions/insertions in a repetitive region without a known function. SOURCE=VEP consequence, Repeat Masker, PFAM

BP4

Multiple lines of computational evidence suggest no impact on gene or gene product (conservation, evolutionary, splicing impact, etc.). SOURCE=SIFT, BLOSUM62, dbscSNV, GERP

BP6

Reputable source recently reports variant as benign but the evidence is not available to the laboratory to perform an independent evaluation. SOURCE=ClinVar, Custom Variant List, Benign
Variants from PMID:31213501

BP7

A synonymous (silent) variant for which splicing prediction algorithms predict no impact to the splice consensus sequence nor the creation of a new splice site AND the nucleotide is nothighly conserved. SOURCE=VEP Consequence, dbscSNV, GERPACMG criteria not implemented: PS2, PS4, PM3, PM6, PP1, PP4, BS2, BS4, BP2, BP5

Appendix 3: Rules for combining criteria to classify variants based on ACMG guidelines
Pathogenic
1.
Uncontrolled when printed

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1. 1 Very Strong (PVS1) AND
1. ≥1 Strong (PS1,PS3) OR
2. ≥2 Moderate (PM1,PM2,PM4,PM5) OR
3. 1 Moderate (PM1,PM2,PM4,PM5) and 1 Supporting (PP2,PP3,PP5) OR
4. ≥2 Supporting (PP2,PP3,PP5)
2. ≥2 Strong (PS1,PS3) OR
3. 1 Strong (PS1,PS3) AND
1. ≥3 Moderate (PM1,PM2,PM4,PM5) OR
2. 2 Moderate (PM1,PM2,PM4,PM5) AND ≥2 Supporting (PP2,PP3,PP5) OR
3. 1 Moderate (PM1,PM2,PM4,PM5) AND ≥3 Supporting (PP2,PP3,PP5)
Likely Pathogenic
1. 1 Very Strong (PVS1) AND 1 Moderate (PM1,PM2,PM4,PM5) OR
2. 1 Strong (PS1,PS3) AND 1-2 Moderate (PM1,PM2,PM4,PM5) OR
3. 1 Strong (PS1,PS3) AND ≥2 (PP2,PP3,PP5) OR
4. ≥3 Moderate (PM1,PM2,PM4,PM5) OR
5. 2 Moderate (PM1,PM2,PM4,PM5) AND ≥2 Supporting (PP2,PP3,PP5) OR
6. 1 Moderate (PM1,PM2,PM4,PM5) and ≥3 Supporting (PP2,PP3,PP5)
Benign1. 1 Stand-Alone (BA1) OR
2. ≥2 Strong (BS2,BS3)
Likely Benign
1. 1 Strong (BS1, BS3) AND 1 Supporting (BP1,BP3,BP4,BP6,BP7) OR2. ≥2 Supporting (BP1,BP3,BP4,BP6,BP7)
Uncertain Significance1. Variants that do not meet the above criteria
2. Conflicting classification labels (eg Likely Pathogenic, Likely Benign) which are listed

Appendix 4: Databases/Software Used
Database/Software

Version Used

PFAM

2022-05-15

Ensembl VEP cache 1000 Genomes

phase3

Ensembl VEP cache SIFT

sift5.2.2

Benign Variants from PMID:31213501

v1.0.0Ensembl VEP cache dbSNP

154

Ensembl VEP cache RefSeq

110

freebayes

1.3.2-38-g71a3e1c-dirty

Custom Variant List

v1.0.0

GEMJ

v1.0.0multiqc

1.8

ClinVar2023-01-09

Human gene annotation

2022-10-04

fastp

0.20.0vep

108.2

dbscSNV

2015-04-13

Ensembl VEP cache assembly

GRCh38.p13

samtools

1.9

Ensembl VEP cache2022-10-07

Repeat Masker database2022-10-19

BLOSUM62108

bwa

0.7.17-r1188

Pathogenic Variants from PMID:31213501

v1.0.0ogtkit

0.8.6

CNV references

v2.0.0

HGMD

v2022.3

sambamba

0.7.1

bedtools

2.29.2

Ensembl VEP cache gnomADe

r2.1.1

GERP

v1.0.0

Human genome reference

2014-01-11

vt

0.5

Ensembl VEP cache GENCODE

GENCODE_42

Appendix 5: Targeted Genes
Gene Symbol

Transcript

Protein

ABCA4

NM_000350.3

NP_000341.2

HGNC ID34

ADGRV1

NM_032119.4

NP_115495.3

17416

AIPL1

NM_014336.5

NP_055151.3

359

BEST1

NM_004183.4

NP_004174.1

12703

C8orf37

NM_177965.4

NP_808880.1

27232

CA4

NM_000717.5

NP_000708.1

1375

CACNA1F

NM_005183.4

NP_005174.2

1393

CDH23

NM_022124.6

NP_071407.4

13733

CDHR1

NM_033100.4

NP_149091.1

14550

CEP290

NM_025114.4

NP_079390.3

29021

CERKL

NM_001030311.3

NP_001025482.1

21699

Uncontrolled when printed

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CFAP410

NM_004928.3

NP_004919.1

CHM

NM_000390.4

NP_000381.1

1260
1940

CLRN1

NM_174878.3

NP_777367.1

12605

CNGA1

NM_000087.5

NP_000078.3

2148

CNGA3

NM_001298.3

NP_001289.1

2150

CNGB1

NM_001297.5

NP_001288.3

2151

CNGB3

NM_019098.5

NP_061971.3

2153

CRB1

NM_201253.3

NP_957705.1

2343

CRX

NM_000554.6

NP_000545.1

2383

CYP4V2

NM_207352.4

NP_997235.3

23198

DHDDS

NM_024887.4

NP_079163.2

20603

DRAM2

NM_178454.6

NP_848549.3

28769

EYS

NM_001292009.2

NP_001278938.1

21555

EYS

NM_001142800.2

NP_001136272.1

21555

FAM161A

NM_001201543.2

NP_001188472.1

25808

FSCN2

NM_001077182.3

NP_001070650.1

3960

GNAT2

NM_005272.5

NP_005263.1

4394

GRK1

NM_002929.3

NP_002920.1

10013

GUCA1A

NM_000409.5

NP_000400.2

4678

GUCY2D

NM_000180.4

NP_000171.1

4689

IDH3B

NM_006899.5

NP_008830.2

5385

IMPDH1

NM_000883.4

NP_000874.2

6052

IMPG2

NM_016247.4

NP_057331.2

18362

IQCB1

NM_001023570.4

NP_001018864.2

28949

KCNV2

NM_133497.4

NP_598004.1

19698

KLHL7

NM_001031710.3

NP_001026880.2

15646

LRAT

NM_004744.5

NP_004735.2

6685

MAK

NM_001242957.3

NP_001229886.1

6816

MERTK

NM_006343.3

NP_006334.2

7027

MYO7A

NM_000260.4

NP_000251.3

7606

NMNAT1

NM_022787.4

NP_073624.2

17877

NR2E3

NM_014249.4

NP_055064.1

7974

NRL

NM_006177.5

NP_006168.1

8002

NYX

NM_022567.3

NP_072089.2

8082

PCARE

NM_001029883.3

NP_001025054.1

34383

PDE6A

NM_000440.3

NP_000431.2

8785

PDE6B

NM_000283.4

NP_000274.3

8786

PDE6C

NM_006204.4

NP_006195.3

8787

PDE6G

NM_002602.4

NP_002593.1

8789

POC1B

NM_172240.3

NP_758440.1

30836
32528

PRCD

NM_001077620.3

NP_001071088.1

PROM1

NM_006017.3

NP_006008.1

9454

PRPF3

NM_004698.4

NP_004689.1

17348

PRPF31

NM_015629.4

NP_056444.3

15446

PRPF6

NM_012469.4

NP_036601.2

15860

PRPF8

NM_006445.4

NP_006436.3

17340

PRPH2

NM_000322.5

NP_000313.2

9942

RBP3

NM_002900.3

NP_002891.1

9921

RDH12

NM_152443.3

NP_689656.2

19977
9940

RDH5

NM_002905.5

NP_002896.2

RGR

NM_001012720.2

NP_001012738.1

9990

RGS9BP

NM_207391.3

NP_997274.2

30304

RHO

NM_000539.3

NP_000530.1

10012

RLBP1

NM_000326.5

NP_000317.1

10024

ROM1

NM_000327.4

NP_000318.2

10254

RP1

NM_006269.2

NP_006260.1

10263

RP1L1

NM_178857.6

NP_849188.4

15946

RP2

NM_006915.3

NP_008846.2

10274

RP9

NM_203288.2

NP_976033.1

10288

RPE65

NM_000329.3

NP_000320.1

10294

RPGR

NM_001034853.2

NP_001030025.1

10295

RPGR

NM_000328.3

NP_000319.1

10295

RPGRIP1

NM_020366.4

NP_065099.3

13436

RS1

NM_000330.4

NP_000321.1

10457

SAG

NM_000541.5

NP_000532.2

10521

SEMA4A

NM_022367.4

NP_071762.2

10729

SNRNP200

NM_014014.5

NP_054733.2

30859

SPATA7

NM_018418.5

NP_060888.2

20423

TOPORS

NM_005802.5

NP_005793.2

21653

TTC8

NM_198309.3

NP_938051.1

20087

TULP1

NM_003322.6

NP_003313.3

12423

Uncontrolled when printed

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USH2A

NM_206933.4

NP_996816.3

12601

ZNF513

NM_144631.6

NP_653232.3

26498

Appendix 6: QC Metrics
Name

Definition

Mapped Reads (%)

The percentage of total reads that are aligned to the reference genome

Duplicated Reads (%)

The percentage of total reads that are marked duplicatedMean Target Coverage

The mean target coverage is defined as the sum of base counts (coverage) within the targeted regions of the panel divided by the total length of these regions. Allbase counts are calculated from filtered, mapped and de-duplicated reads

Low Coverage (>=100x)

The percentage of bases that have a coverage above or equal to 100

Medium Coverage

The percentage of bases that have a coverage above or equal to 500

High Coverage

The percentage of bases that have a coverage above or equal to 1000

Evenness

The evenness score represents the fraction of whole-sequencing throughput that is correctly distributed over the targeted regions of the panel

Average Quality

The average base Phred quality score of all reads

Average Insert Size

The average absolute template length for paired and mapped reads

Insert Size std

The standard deviation of the average template length distribution

Reads Mapping Quality 0 (%)

The percentage of total reads that have a mapping quality equal to 0

Targets Not Covered

The number of targeted regions of the panel that have coverage below the specified value of 1

On Target Reads (%)

The percentage of filtered aligned reads that are overlapping on all regions defined in the panel

On And Near Target Reads(%)

The percentage of filtered aligned reads that are overlapping on all regions defined in the panel by 250bp in both directions

Off Target Reads (%)

The percentage of filtered aligned reads that are not overlapping on-target or near-on-target regions defined in the panel

Uniformity

The fold of additional sequencing required to ensure that 80% of the target bases achieve the mean coverage

Pipeline-Calculated Sample
Sex

The chromosomal sex predicted based on the coverage of targeted regions from sex chromosomes

Customer-Provided Sex

Sex of the sample as provided by the customer

Derivative Log Ratio Score
for IRD System

Derivative spread of the log2 ratios of comparative read depth values used for CNV calling

Appendix 7: QC Thresholds
Name

Pass

Mapped Reads (%)*>=95.0Mean Target Coverage>=240.0

Low Coverage (>=100x)>=95.0Evenness>=75.0Targets Not Covered*<=30.0On Target Reads (%)>=60.0* Metric not included in sample pass/fail criteria

Uncontrolled when printed

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神戸市中央区脇浜海岸通1-5-1 〒651-0073

Uncontrolled when printed

79/79

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