owencqueen/cgbench_data huggingface dataset:
Gene: RPE65 (HGNC:10294)
Evidence Code: PVS1 — Original ACMG Summary
Null variant (nonsense, frameshift, canonical +/−1 or 2 splice sites, initiation codon, single or multi-exon deletion) in a gene where loss of function (LOF) is a known mechanism of disease.
Caveats:
 • Beware of genes where LOF is not a known disease mechanism (e.g. GFAP, MYH7).
 • Use caution interpreting LOF variants at the extreme 3’ end of a gene.
 • Use caution with splice variants that are predicted to lead to exon skipping but leave the remainder of the protein intact.
 • Use caution in the presence of multiple transcripts.
Gene: RPE65 (HGNC:10294)
Evidence Code: PVS1 — Very Strong
Modification Type: Gene-specific
Null variant in a gene where loss of function is a known mechanism of disease.




Use as defined by ClinGen SVI working group 
16
 and as updated by the ClinGen SVI Splicing Subgroup 
17


Refer to RPE65-specific PVS1 Decision Tree, file attached.


PVS1: Predicted splice defects at +/- 1,2 in exons 1-14


PVS1: Single to multi-exon deletions, with or without predicted NMD. All exons are considered critical to protein function.


PVS1: Nonsense or frameshift mutations from p.Ser2 through p.Gly528


PVS1: Duplications of exons proven in tandem


PVS1(RNA): RNA splicing data with evidence of alternative transcript production at complete levels, relative to normal allele.
Gene: RPE65 (HGNC:10294)
Evidence Code: PVS1 — Strong
Modification Type: Gene-specific
Null variant in a gene where loss of function is a known mechanism of disease.




Use as defined by ClinGen SVI working group 
16
 and as updated by the ClinGen SVI Splicing Subgroup 
17


Refer to RPE65-specific PVS1 Decision Tree, file attached.


PVS1_Strong:Applied to variants in the initiation codon. The second in-frame methionine is located at residue 93, and there is no known study indicating that this methionine in 
RPE65
 can be used as start codon. Variants affecting Met1 can lead to a complete absence of the protein product. Even though we cannot exclude the possibility of a 2nd Met being used as start codon, the translation efficiency maybe significantly reduced due to lack of other important elements (Kozak sequence, etc.). Also, there are multiple variants located upstream of Met93 having been reported as a pathogenic variant in HGMD and ClinVar, evidence that this region of the protein is functionally important.


PVS1_Strong: Nonsense or frameshift mutations from p.Leu529 through p.Ser533


PVS1_Strong: Duplications of exons presumed in tandem


PVS1(RNA)_Strong: RNA splicing data with evidence of alternative transcript production at near complete levels, relative to normal allele.
Gene: RPE65 (HGNC:10294)
Evidence Code: PS1 — Original ACMG Summary
Same amino acid change as a previously established pathogenic variant regardless of nucleotide change.
Example: Val->Leu caused by either G>C or G>T in the same codon.
Caveat: Beware of changes that impact splicing rather than at the amino acid/protein level.
Gene: RPE65 (HGNC:10294)
Evidence Code: PS1 — Strong
Modification Type: Gene-specific
Same amino acid change as a previously established Pathogenic variant regardless of nucleotide change.




Must have one comparison variant that reaches a Pathogenic classification using this rule specification.


For assessing same amino acid changes, SpliceAI scores for both variants should be within 10% of each other.




Same predicted splicing impact as a previously classified Pathogenic variant. 




Used in conjunction with PP3 for variants located outside the splice donor/acceptor +/-1,2 dinucleotide positions that have a splice AI score ≥0.2 and have a comparable nucleotide variant at the 
same position
 that has been designated 
Pathogenic
.


Used in conjunction with PVS1 for variants located at the splice donor/acceptor +/-1,2 dinucleotide positions and that have a comparable variant within the same splice donor/acceptor +/-1,2 dinucleotide that has been designated Pathogenic.




Specific combinations are found in RPE65-specific PVS1 Decision Tree 
part (b)
 (Table 2 from Walker 2023).
Gene: RPE65 (HGNC:10294)
Evidence Code: PS1 — Moderate
Modification Type: Gene-specific,Strength
Same amino acid change as a previously established Likely Pathogenic variant regardless of nucleotide change.




Must have one comparison variant that reaches a Likely Pathogenic classification using this rule specification.


For assessing same amino acid changes, SpliceAI scores for both variants should be within 10% of each other.




Same predicted splicing impact as previously classified Likely Pathogenic variant.




Used in conjunction with PP3 for variants located outside the splice donor/acceptor +/-1,2 dinucleotide positions that have a splice AI score ≥0.2 and have a comparable nucleotide variant at the 
same position
 that has been designated 
Likely Pathogenic
.


Used in conjunction with PVS1_(reduced strength) for variants located at the splice donor/acceptor +/-1,2 dinucleotide positions and have a comparable variant 
within the same splice donor/acceptor motif
 (but outside the +/-1,2 dinucleotide) that has been designated 
Pathogenic
.




Specific combinations are found in RPE65-specific PVS1 Decision Tree 
part (b)
 (Table 2 from Walker 2023).
Gene: RPE65 (HGNC:10294)
Evidence Code: PS1 — Supporting
Modification Type: Gene-specific,Strength
Used in conjunction with PP3 for variants located outside the splice donor/acceptor +/-1,2 dinucleotide positions that have a splice AI score ≥0.2 and have a comparable nucleotide variant within the 
same motif
 that has been designated 
Likely Pathogenic
.


Used in conjunction with PVS1 or PVS1_(reduced strength) for variants located at the splice donor/acceptor +/-1,2 dinucleotide positions and have a comparable Likely Pathogenic or Pathogenic variant either within the same splice site donor/acceptor motif, outside the +/-1,2 dinucleotide, or at the +/-1,2 dinucleotide.




 Specific combinations are found in RPE65-specific PVS1 Decision Tree 
part (b)
 (Table 2 from Walker 2023).
Gene: RPE65 (HGNC:10294)
Evidence Code: PS2 — Original ACMG Summary
De novo (both maternity and paternity confirmed) in a patient with the disease and no family history.
Note: Confirmation of paternity only is insufficient. Egg donation, surrogate motherhood, errors in embryo transfer, etc. can contribute to non-maternity.
Gene: RPE65 (HGNC:10294)
Evidence Code: PS2 — Very Strong
Modification Type: Gene-specific
De novo (
both
 maternity and paternity confirmed) in a patient with the disease and no family history.




Use ClinGen SVI's recommendation for assigning weight to the PS2/PM6 codes (See PS2-Table 1 within PS2/PM6 file). Use option 3 “Phenotype consistent with gene but not highly specific and high genetic heterogeneity” (maximum 0.5 points/proband)


Total of 4 or more points required for Very Strong level
Gene: RPE65 (HGNC:10294)
Evidence Code: PS2 — Strong
Modification Type: Gene-specific
De novo (
both
 maternity and paternity confirmed) in a patient with the disease and no family history.




Use ClinGen SVI's recommendation for assigning weight to the PS2/PM6 codes (See PS2-Table 1 within PS2/PM6 file). Use option 3 “Phenotype consistent with gene but not highly specific and high genetic heterogeneity” (maximum 0.5 points/proband)


Total of 2.00 - 3.75 points required for Strong level
Gene: RPE65 (HGNC:10294)
Evidence Code: PS2 — Moderate
Modification Type: Gene-specific
De novo (
both
 maternity and paternity confirmed) in a patient with the disease and no family history.




Use ClinGen SVI's recommendation for assigning weight to the PS2/PM6 codes (See PS2-Table 1 within PS2/PM6 file). Use option 3 “Phenotype consistent with gene but not highly specific and high genetic heterogeneity” (maximum 0.5 points/proband)


Total of 1.00 - 1.75 points required for Moderate level
Gene: RPE65 (HGNC:10294)
Evidence Code: PS2 — Supporting
Modification Type: Gene-specific
De novo (
both
 maternity and paternity confirmed) in a patient with the disease and no family history.




Use ClinGen SVI's recommendation for assigning weight to the PS2/PM6 codes (See Table 1 within PS2/PM6 file). Use option 3 “Phenotype consistent with gene but not highly specific and high genetic heterogeneity” (maximum 0.5 points/proband)


Total of 0.50 - 0.75 points required for Supporting level
Gene: RPE65 (HGNC:10294)
Evidence Code: PS3 — Original ACMG Summary
Well-established in vitro or in vivo functional studies supportive of a damaging effect on the gene or gene product.
Note: Functional studies that have been validated and shown to be reproducible and robust in a clinical diagnostic laboratory setting are considered the most well-established.
Gene: RPE65 (HGNC:10294)
Evidence Code: PS3 — Supporting
Modification Type: Gene-specific,Strength
Well-established in vitro or in vivo functional studies supportive of a damaging effect. Not applicable for splicing effects (replaced by PVS1_Strength (RNA))


See attached table for acceptable functional studies.


For studies reporting isomerhydrolase activity, cutoff is ≤10% of wild-type control.
Gene: RPE65 (HGNC:10294)
Evidence Code: PS4 — Original ACMG Summary
The prevalence of the variant in affected individuals is significantly increased compared to the prevalence in controls.
Note 1: Relative risk (RR) or odds ratio (OR), as obtained from case-control studies, is >5.0 and the confidence interval around the estimate of RR or OR does not include 1.0. See manuscript for detailed guidance.
Note 2: In instances of very rare variants where case-control studies may not reach statistical significance, the prior observation of the variant in multiple unrelated patients with the same phenotype, and its absence in controls, may be used as moderate level of evidence.
Gene: RPE65 (HGNC:10294)
Evidence Code: PM1 — Original ACMG Summary
Located in a mutational hot spot and/or critical and well-established functional domain (e.g. active site of an enzyme) without benign variation.
Gene: RPE65 (HGNC:10294)
Evidence Code: PM1 — Moderate
Modification Type: Gene-specific
Located in a mutational hot spot and/or critical and well-established functional domain.




Met by variants encoding missense substitutions at His180, His182, His241, His313, Glu417, or His527, which are required residues located within the active site
16
.


Met by variants encoding missense substitutions between Ala107 and Gly125, which are known to mediate localization to the ER membrane
15
.
Gene: RPE65 (HGNC:10294)
Evidence Code: PM2 — Original ACMG Summary
Absent from controls (or at extremely low frequency if recessive) in Exome Sequencing Project, 1000 Genomes or Exome Aggregation Consortium.
Caveat: Population data for indels may be poorly called by next generation sequencing.
Gene: RPE65 (HGNC:10294)
Evidence Code: PM2 — Supporting
Modification Type: Disease-specific,Strength
Absent/rare from controls in an ethnically-matched cohort population sample.




Used if the gnomAD PopMax Filtering Allele Frequency (FAF) is ≤ 2.0 x 10
-4
.
Gene: RPE65 (HGNC:10294)
Evidence Code: PM3 — Original ACMG Summary
For recessive disorders, detected in trans with a pathogenic variant
Note: This requires testing of parents (or offspring) to determine phase.
Gene: RPE65 (HGNC:10294)
Evidence Code: PM3 — Very Strong
Modification Type: Disease-specific
Points are calculated using Table 1 from 
https://clinicalgenome.org/site/assets/files/3717/svi_proposal_for_pm3_criterion_-_version_1.pdf
 (or attached file “PM3 Tables”)




≥4 points from Table 1
Gene: RPE65 (HGNC:10294)
Evidence Code: PM3 — Strong
Modification Type: Disease-specific
Points are calculated using Table 1 from 
https://clinicalgenome.org/site/assets/files/3717/svi_proposal_for_pm3_criterion_-_version_1.pdf
 (or attached file “PM3 Tables”)




 2 to 3.75 points from Table 1
Gene: RPE65 (HGNC:10294)
Evidence Code: PM3 — Moderate
Modification Type: Disease-specific
Points are calculated using Table 1 from 
https://clinicalgenome.org/site/assets/files/3717/svi_proposal_for_pm3_criterion_-_version_1.pdf
 (or attached file “PM3 Tables”)




 1 to 1.75 points from Table 1
Gene: RPE65 (HGNC:10294)
Evidence Code: PM3 — Supporting
Modification Type: Disease-specific
Points are calculated using Table 1 from 
https://clinicalgenome.org/site/assets/files/3717/svi_proposal_for_pm3_criterion_-_version_1.pdf
 (or attached file “PM3 Tables”)




 0.5 to 0.75 points from Table 1
Gene: RPE65 (HGNC:10294)
Evidence Code: PM4 — Original ACMG Summary
Protein length changes due to in-frame deletions/insertions in a non-repeat region or stop-loss variants.
Gene: RPE65 (HGNC:10294)
Evidence Code: PM4 — Moderate
Modification Type: Gene-specific
Protein length changes due to in-frame deletions/insertions in a non-repeat region or stop-loss variants.




 Protein length change of ≥2 amino acids that leads to loss of at least one conserved residue (PhyloP>2.0) or insertion of new amino acids adjacent to at least one conserved residue (PhyloP>2.0).
Gene: RPE65 (HGNC:10294)
Evidence Code: PM4 — Supporting
Modification Type: Gene-specific,Strength
Protein length changes due to in-frame deletions/insertions in a non-repeat region or stop-loss variants.




 Protein length change of 1 amino acid that leads to loss of at least one conserved residue (PhyloP>2.0) or insertion of new amino acid adjacent to at least one conserved residue (PhyloP>2.0).
Gene: RPE65 (HGNC:10294)
Evidence Code: PM5 — Original ACMG Summary
Novel missense change at an amino acid residue where a different missense change determined to be pathogenic has been seen before.
Example: Arg156His is pathogenic; now you observe Arg156Cys.
Caveat: Beware of changes that impact splicing rather than at the amino acid/protein level.
Gene: RPE65 (HGNC:10294)
Evidence Code: PM5 — Moderate
Modification Type: None
Missense change at an amino acid residue where a different missense change determined to be pathogenic has been seen before.




Must have one comparison variant that reaches a Pathogenic classification using this rule specification.


For assessing same amino acid changes, SpliceAI scores for both variants should be within 10% of each other.
Gene: RPE65 (HGNC:10294)
Evidence Code: PM5 — Supporting
Modification Type: Strength
Missense change at an amino acid residue where a different missense change determined to be pathogenic has been seen before.




Must have one comparison variant that reaches a Likely Pathogenic classification using this rule specification.


For assessing same amino acid changes, SpliceAI scores for both variants should be within 10% of each other.
Gene: RPE65 (HGNC:10294)
Evidence Code: PM6 — Original ACMG Summary
Assumed de novo, but without confirmation of paternity and maternity.
Gene: RPE65 (HGNC:10294)
Evidence Code: PP1 — Original ACMG Summary
Co-segregation with disease in multiple affected family members in a gene definitively known to cause the disease.
Note: May be used as stronger evidence with increasing segregation data.
Gene: RPE65 (HGNC:10294)
Evidence Code: PP1 — Strong
Modification Type: Disease-specific,Strength
Co-segregation with disease in multiple affected family members and evidence that this variant and another RPE65 variant are 
in trans
.




Requires segregation in proband plus ≥3 similarly affected relatives
Gene: RPE65 (HGNC:10294)
Evidence Code: PP1 — Moderate
Modification Type: Disease-specific,Strength
Co-segregation with disease in multiple affected family members and evidence that this variant and another RPE65 variant are 
in trans
.




Requires segregation in proband plus 2 similarly affected relatives
Gene: RPE65 (HGNC:10294)
Evidence Code: PP1 — Supporting
Modification Type: Disease-specific,Strength
Co-segregation with disease in multiple affected family members and evidence that this variant and another RPE65 variant are 
in trans
.




Requires segregation in proband plus 1 similarly affected relative
Gene: RPE65 (HGNC:10294)
Evidence Code: PP2 — Original ACMG Summary
Missense variant in a gene that has a low rate of benign missense variation and where missense variants are a common mechanism of disease.
Gene: RPE65 (HGNC:10294)
Evidence Code: PP3 — Original ACMG Summary
Multiple lines of computational evidence support a deleterious effect on the gene or gene product (conservation, evolutionary, splicing impact, etc.).
Caveat: As many in silico algorithms use the same or very similar input for their predictions, each algorithm should not be counted as an independent criterion. PP3 can be used only once in any evaluation of a variant.
Gene: RPE65 (HGNC:10294)
Evidence Code: PP3 — Moderate
Modification Type: Gene-specific,Strength
For a missense variant use REVEL, requires a score of ≥ 0.774.


Splice variants use PP3 only at Supporting level.
Gene: RPE65 (HGNC:10294)
Evidence Code: PP3 — Supporting
Modification Type: Gene-specific
For a missense variant use REVEL, requires a score of 0.644 - 0.773.


For a predicted splicing variant use SpliceAI with max distance set to 500 bp. Highest delta score from SpliceAI must be ≥ 0.2 to use this code. See RPE65-specific PVS1 Decision Tree 
part (a)
 for SpliceAI flowchart.
Gene: RPE65 (HGNC:10294)
Evidence Code: PP4 — Original ACMG Summary
Patient’s phenotype or family history is highly specific for a disease with a single genetic etiology.
Gene: RPE65 (HGNC:10294)
Evidence Code: PP4 — Moderate
Modification Type: Disease-specific,Strength
8 phenotype points or more are required to use this code at the moderate strength for a single proband (see points list below).


Additionally, at least one 
specific
 criterion must be met (see below).


Do not include a proband with a suspected diagnosis of more than one retinal dystrophy.
Gene: RPE65 (HGNC:10294)
Evidence Code: PP4 — Supporting
Modification Type: Disease-specific
4-7.5 phenotype points are required to use this code (see points list below).


Do not include a proband with a suspected diagnosis of more than one retinal dystrophy.
Gene: RPE65 (HGNC:10294)
Evidence Code: PP5 — Original ACMG Summary
Reputable source recently reports variant as pathogenic, but the evidence is not available to the laboratory to perform an independent evaluation.
Gene: RPE65 (HGNC:10294)
Evidence Code: BA1 — Original ACMG Summary
Allele frequency is above 5% in Exome Sequencing Project, 1000 Genomes or Exome Aggregation Consortium.
Gene: RPE65 (HGNC:10294)
Evidence Code: BA1 — Stand Alone
Modification Type: Disease-specific
Use gnomAD PopMax FAF if available, cutoff of  ≥8 x 10
-3




Use large population databases (i.e. gnomAD).
Gene: RPE65 (HGNC:10294)
Evidence Code: BS1 — Original ACMG Summary
Allele frequency is greater than expected for disorder.
Gene: RPE65 (HGNC:10294)
Evidence Code: BS1 — Strong
Modification Type: Disease-specific
Allele frequency greater than expected for disorder. Use gnomAD PopMax FAF if available.




Allele frequency of between 8x10
-3
 and 8x10
-4
Gene: RPE65 (HGNC:10294)
Evidence Code: BS2 — Original ACMG Summary
Observed in a healthy adult individual for a recessive (homozygous), dominant (heterozygous), or X-linked (hemizygous) disorder, with full penetrance expected at an early age.
Gene: RPE65 (HGNC:10294)
Evidence Code: BS2 — Strong
Modification Type: Disease-specific
Variant is present in ≥ 3 homozygotes without any features of the phenotype. This rule only applies to individuals found in the literature who have been well-phenotyped  and are unaffected by age 40.


Presence in databases such as gnomAD are not considered.
Gene: RPE65 (HGNC:10294)
Evidence Code: BS3 — Original ACMG Summary
Well-established in vitro or in vivo functional studies show no damaging effect on protein function or splicing.
Gene: RPE65 (HGNC:10294)
Evidence Code: BS3 — Supporting
Modification Type: Gene-specific,Strength
Well-established in vitro or in vivo functional studies shows no damaging effect on protein function. Not applicable for splicing effects (replaced by BP7_Strong (RNA)).


See attached table for list of acceptable functional studies.


For studies reporting isomerohydrolase activity, activity must be ≥50% of wild-type control.
Gene: RPE65 (HGNC:10294)
Evidence Code: BS4 — Original ACMG Summary
Lack of segregation in affected members of a family.
Caveat: The presence of phenocopies for common phenotypes (i.e. cancer, epilepsy) can mimic lack of segregation among affected individuals. Also, families may have more than one pathogenic variant contributing to an autosomal dominant disorder, further confounding an apparent lack of segregation.
Gene: RPE65 (HGNC:10294)
Evidence Code: BS4 — Strong
Modification Type: Clarification
Lack of segregation in affected members of a family.




One or both variants are absent in a similarly affected family member.
Gene: RPE65 (HGNC:10294)
Evidence Code: BP1 — Original ACMG Summary
Missense variant in a gene for which primarily truncating variants are known to cause disease.
Gene: RPE65 (HGNC:10294)
Evidence Code: BP2 — Original ACMG Summary
Observed in trans with a pathogenic variant for a fully penetrant dominant gene/disorder or observed in cis with a pathogenic variant in any inheritance pattern.
Gene: RPE65 (HGNC:10294)
Evidence Code: BP2 — Supporting
Modification Type: Disease-specific
Observed in cis with a Pathogenic variant.




Use code if the variant of interest is 
in cis
 with a Pathogenic or Likely Pathogenic variant. The other variant must meet a Likely Pathogenic or Pathogenic classification using these rule specifications.
Gene: RPE65 (HGNC:10294)
Evidence Code: BP3 — Original ACMG Summary
In frame-deletions/insertions in a repetitive region without a known function.
Gene: RPE65 (HGNC:10294)
Evidence Code: BP4 — Original ACMG Summary
Multiple lines of computational evidence suggest no impact on gene or gene product (conservation, evolutionary, splicing impact, etc)
Caveat: As many in silico algorithms use the same or very similar input for their predictions, each algorithm cannot be counted as an independent criterion. BP4 can be used only once in any evaluation of a variant.
Gene: RPE65 (HGNC:10294)
Evidence Code: BP4 — Moderate
Modification Type: Gene-specific,Strength
For a missense variant use REVEL, requires a score of ≤0.183. In addition, highest SpliceAI delta score should also be below cutoff of 0.1.
Gene: RPE65 (HGNC:10294)
Evidence Code: BP4 — Supporting
Modification Type: Gene-specific
For a missense variant use REVEL, requires a score between 0.183 - 0.290. In addition, highest SpliceAI delta score should also be below cutoff of 0.1.


For a silent / intronic variant outside the designated splice region (conservatively at or beyond positions +7/-21) and synonymous (silent) exonic variants located outside of the first and the last 3 bases of the exon, BP4 can be met if the highest of the four delta scores within SpliceAI is below the cutoff of ≤0.1. See RPE65-specific PVS1 Decision Tree 
part (a)
 for SpliceAI flowchart.




Please note that BP7 can be met as well.
Gene: RPE65 (HGNC:10294)
Evidence Code: BP5 — Original ACMG Summary
Variant found in a case with an alternate molecular basis for disease.
Gene: RPE65 (HGNC:10294)
Evidence Code: BP6 — Original ACMG Summary
Reputable source recently reports variant as benign, but the evidence is not available to the laboratory to perform an independent evaluation.
Gene: RPE65 (HGNC:10294)
Evidence Code: BP7 — Original ACMG Summary
A synonymous 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 not highly conserved.
Gene: RPE65 (HGNC:10294)
Evidence Code: BP7 — Strong
Modification Type: Disease-specific
BP7_Strong (RNA) Used to designate capture of splicing data (not BS3). See RPE65-specific PVS1 Decision Tree, file attached, for weighting and combining with other codes.
Gene: RPE65 (HGNC:10294)
Evidence Code: BP7 — Supporting
Modification Type: Gene-specific
Use for variants located outside of the donor/acceptor +/- 1,2 dinucleotide positions. 


If SpliceAI score ≤0.1, apply BP4 followed by assessment of BP7. See RPE65-specific PVS1 Decision Tree 
part (a)
 for SpliceAI flowchart.




Positions 
excluded
 from BP7:


Synonymous substitutions at the first base of an exon


Synonymous substitutions in the last 3 bases of an exon


+1 through +7 of donor sequence


-1 through -21 of acceptor sequence