owencqueen/cgbench_data huggingface dataset:
Gene: GATM (HGNC:4175)
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: GATM (HGNC:4175)
Evidence Code: PVS1 — Very Strong
Modification Type: None
Nonsense-mediated decay predicted.


CCDS VCEP notes:
Loss of function (LOF) of GATM is a known mechanism of disease for arginine:glycine amidinotransferase deficiency (AGAT-D). There are examples of various LOF variants, including nonsense and frameshift, in GATM in individuals with AGAT-D (
https://databases.lovd.nl/shared/variants/GATM/unique
). The specifications below are based on the PVS1 decision tree (Figure 1, Abou Tayoun et al, 2018, PMID 30192042).


GATM specifications:
Nonsense and frameshift variants
* All nonsense and frameshift variants will meet PVS1 unless a premature termination codon is predicted to be missed by nonsense-mediated decay (NMD) because it is located in the last exon (exon 9) or the last 50 bases of the penultimate exon (exon 8, 3’ of c.1109). In that case, PVS1_Strong or PVS1_Moderate will be applied depending on whether >10% or <10% of the protein is lost.


Splice site variants (+1, +2, -1, -2)
* All canonical splice site pairs in GATM are GT-AG.
* For any canonical splice site variant (+1, +2, -1, -2), the exon immediately adjacent to the variant is predicted to be skipped i.e. upstream exon skipped for canonical donor splice site variants and downstream exon skipped for canonical acceptor splice site variants.
* For the predicted in frame/out of frame consequences of exon skipping and considerations for strength of PVS1, see 
Appendix 1
.
* If this criterion is applied, PP3 (in silico splice site prediction tools) should not be used.
* To apply PVS1, splice site variants must have no detectable nearby (+/- 20 nucleotides) strong consensus splice sequence that may reconstitute in-frame splicing. Otherwise, the PVS1 strength should be reduced accordingly.
* Non-canonical splice variants, such as +3 or -3, will not meet PVS1, but could meet PS3 and/or PP3 criteria.


Deletions (single or multi exon)
* If a single or multi-exon deletion results in an out of frame consequence, use PVS1 unless not predicted to undergo NMD. If not predicted to undergo NMD, use PVS1_Strong if >10% of the protein is predicted to be removed, and use PVS1_Moderate if <10% of the protein is predicted to be removed.
* If the consequence is in frame, the deletion must encompass one or more exons for PVS1 to apply. Use PVS1_Strong if more than 10% of the protein is removed and PVS1_Moderate if <10% of the protein is removed.
* If the in frame deletion is smaller than one exon, PVS1 does not apply; consider using PM4.
* 
Appendix 1
 can be used to predict the consequences of single exon deletions.


Duplications
* Use the PVS1 decision tree (Figure 1, Abou Tayoun et al, 2018, PMID 30192042) to assess the impact of duplications.
Gene: GATM (HGNC:4175)
Evidence Code: PVS1 — Strong
Modification Type: Strength
In frame loss of >10% of the protein.
CCDS VCEP notes:
Loss of function (LOF) of GATM is a known mechanism of disease for arginine:glycine amidinotransferase deficiency (AGAT-D). There are examples of various LOF variants, including nonsense and frameshift, in GATM in individuals with AGAT-D (
https://databases.lovd.nl/shared/variants/GATM/unique
). The specifications below are based on the PVS1 decision tree (Figure 1, Abou Tayoun et al, 2018, PMID 30192042).


GATM specifications:
Nonsense and frameshift variants
* All nonsense and frameshift variants will meet PVS1 unless a premature termination codon is predicted to be missed by nonsense-mediated decay (NMD) because it is located in the last exon (exon 9) or the last 50 bases of the penultimate exon (exon 8, 3’ of c.1109). In that case, PVS1_Strong or PVS1_Moderate will be applied depending on whether >10% or <10% of the protein is lost.


Splice site variants (+1, +2, -1, -2)
* All canonical splice site pairs in GATM are GT-AG.
* For any canonical splice site variant (+1, +2, -1, -2), the exon immediately adjacent to the variant is predicted to be skipped i.e. upstream exon skipped for canonical donor splice site variants and downstream exon skipped for canonical acceptor splice site variants.
*Use SpliceAI and varSEAK to look for nearby (+/- 20 nucleotides) strong consensus splice sequence that may reconstitute in-frame splicing. 
* For considerations for strength at which PVS1 may be applied see 
Appendix 1
.
* If this criterion is applied, PP3 (in silico splice site prediction tools) should not be used.
* Non-canonical splice variants, such as +3 or -3, will not meet PVS1, but could meet PS3 and/or PP3 criteria.


Deletions (single or multi exon)
* If a single or multi-exon deletion results in an out of frame consequence, use PVS1 unless not predicted to undergo NMD. If not predicted to undergo NMD, use PVS1_Strong if >10% of the protein is predicted to be removed, and use PVS1_Moderate if <10% of the protein is predicted to be removed.
* If the consequence is in frame, the deletion must encompass one or more exons for PVS1 to apply. Use PVS1_Strong if more than 10% of the protein is removed and PVS1_Moderate if <10% of the protein is removed.
* If the in frame deletion is smaller than one exon, PVS1 does not apply; consider using PM4.
* 
Appendix 1
 can be used to predict the consequences of single exon deletions.


Duplications
* Use the PVS1 decision tree (Figure 1, Abou Tayoun et al, 2018, PMID 30192042) to assess the impact of duplications.
Gene: GATM (HGNC:4175)
Evidence Code: PVS1 — Moderate
Modification Type: Strength
Single exon or larger deletion resulting in loss of <10% of the protein, and initiator codon variants.


CCDS VCEP notes:
Loss of function (LOF) of GATM is a known mechanism of disease for arginine:glycine amidinotransferase deficiency (AGAT-D). There are examples of various LOF variants, including nonsense and frameshift, in GATM in individuals with AGAT-D (
https://databases.lovd.nl/shared/variants/GATM/unique
). The specifications below are based on the PVS1 decision tree (Figure 1, Abou Tayoun et al, 2018, PMID 30192042).  


GATM specifications:


Nonsense and frameshift variants
* All nonsense and frameshift variants will meet PVS1 unless a premature termination codon is predicted to be missed by nonsense-mediated decay (NMD) because it is located in the last exon (exon 9) or the last 50 bases of the penultimate exon (exon 8, 3’ of c.1109). In that case, PVS1_Moderate will be applied.


Splice site variants (+1, +2, -1, -2)
* All canonical splice site pairs in GATM are GT-AG.
* For any canonical splice site variant (+1, +2, -1, -2), the exon immediately adjacent to the variant is predicted to be skipped i.e. upstream exon skipped for canonical donor splice site variants and downstream exon skipped for canonical acceptor splice site variants.
*Use SpliceAI and varSEAK to look for nearby (+/- 20 nucleotides) strong consensus splice sequence that may reconstitute in-frame splicing. 
* For considerations for strength at which PVS1 may be applied see 
Appendix 1
.
* If this criterion is applied, PP3 (in silico splice site prediction tools) should not be used.
* Non-canonical splice variants, such as +3 or -3, will not meet PVS1, but could meet PS3 and/or PP3 criteria.


Initiator codon variants
* To our knowledge, initiator codon variants have not been reported in GATM (01/2019) but may occur.
* All initiator codon variants will meet PVS1_Moderate. The next in-frame methionine is at amino acid position 130 (based on NP_001473).


Deletions (single or multi exon)
* If a single or multi-exon deletion results in an out of frame consequence, use PVS1 unless not predicted to undergo NMD. If not predicted to undergo NMD, use PVS1_Strong if >10% of the protein is predicted to be removed, and use PVS1_Moderate if <10% of the protein is predicted to be removed.
* If the consequence is in frame, the deletion must encompass one or more exons for PVS1 to apply. Use PVS1_Strong if more than 10% of the protein is removed and PVS1_Moderate if <10% of the protein is removed.
* If the in frame deletion is smaller than one exon, PVS1 does not apply; consider using PM4.
* 
Appendix 1
 can be used to predict the consequences of single exon deletions.


Duplications
* Use the PVS1 decision tree (Figure 1, Abou Tayoun et al, 2018, PMID 30192042) to assess the impact of duplications.
Gene: GATM (HGNC:4175)
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: GATM (HGNC:4175)
Evidence Code: PS1 — Strong
Modification Type: None
This criterion is applicable as described.


If the variant is in the last 3 nucleotides of an exon, further analysis using splicing site prediction algorithms (see PP3) and data from the literature (if available) is required to investigate the impact on splicing.
Gene: GATM (HGNC:4175)
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: GATM (HGNC:4175)
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: GATM (HGNC:4175)
Evidence Code: PS3 — Strong
Modification Type: Disease-specific
RT-PCR evidence of mis-splicing for non-canonical intronic variants with no evidence of normal splice products.


GATM specifications:
Any variant meeting the description for either in vitro expression or splicing assays can meet PS3 at the strengths given. If a variant meets the description for both e.g., a splice site variant with no evidence of abnormal splicing and deficient AGAT activity in vitro, PS3 must only be applied once.


Splicing assays
For non-canonical splicing variants, use PS3 if there is RT-PCR and/or RNA sequencing evidence demonstrating only abnormal splice products, with no evidence of normal splicing.
* Evidence of abnormal splicing includes transcripts of alternative length or with specific intron or exon inclusion/exclusion. These studies can be performed on mRNA extracted from patient-derived cells, or by inserting the mutant genomic DNA into plasmid vectors and introducing these into human or other mammalian host cells.
* Note that in patients who are compound heterozygotes for a splicing variant and another variants type that does not disrupt splicing, such as a missense variant, evidence of normal splicing is expected. However, the presence of normal splice products could complicate the assessment of the impact of the splice variant. Therefore, if there is any evidence of normal splice products, either when using RNA from patient cells or in an in vitro expression system, use PS3_Supporting.
* PP3 may also be used for non-canonical splice variants meeting PS3 or PS3_Supporting.
Gene: GATM (HGNC:4175)
Evidence Code: PS3 — Supporting
Modification Type: Disease-specific
<15% control activity when variant is expressed in HeLa cells, as reported in PMID 27233232.
RT-PCR evidence of mis-splicing for non-canonical intronic variants with evidence of normal splice products.


GATM specifications:
Any variant meeting the description for either in vitro expression or splicing assays can meet PS3 at the strengths given. If a variant meets the description for both e.g., a splice site variant with no evidence of abnormal splicing and deficient AGAT activity in vitro, PS3 must only be applied once.  


In vitro expression
AGAT activity data from an in vitro assay in which GATM variants were overexpressed in HeLa cells has been published (DesRoches et al, 2016; PMID 27233232). Any variant with AGAT activity at or below 15% of normal in this paper meets PS3_Supporting (see 
Appendix 2
 for further details on AGAT functional assays).  


Splicing assays
For non-canonical splicing variants, use PS3 if there is RT-PCR and/or RNA sequencing evidence demonstrating only abnormal splice products, with no evidence of normal splicing.
* Evidence of abnormal splicing includes transcripts of alternative length or with specific intron or exon inclusion/exclusion. These studies can be performed on mRNA extracted from patient-derived cells, or by inserting the mutant genomic DNA into plasmid vectors and introducing these into human or other mammalian host cells.
* Note that in patients who are compound heterozygotes for a splicing variant and another variants type that does not disrupt splicing, such as a missense variant, evidence of normal splicing is expected. However, the presence of normal splice products could complicate the assessment of the impact of the splice variant. Therefore, if there is any evidence of normal splice products, either when using RNA from patient cells or in an in vitro expression system, use PS3_Supporting.
* PP3 may also be used for non-canonical splice variants meeting PS3 or PS3_Supporting.
Gene: GATM (HGNC:4175)
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: GATM (HGNC:4175)
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: GATM (HGNC:4175)
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: GATM (HGNC:4175)
Evidence Code: PM2 — Supporting
Modification Type: Disease-specific,Strength
Allele frequency <0.000055 (<0.0055%) in all populations in gnomAD.


CCDS VCEP notes: It is acceptable for a GATM variant to be present in controls, if heterozygous, because AGAT-D is a recessive disorder. Homozygotes should not be seen in a population database, such as gnomAD, because the penetrance of this condition in individuals with biallelic pathogenic variants is expected to be 100%. 


GATM specifications:




All subpopulations in gnomAD must have a maximum allele frequency less than 0.000055 (based on the prevalence of the most common suspected pathogenic variants, c.484+1G>T and p.Arg169Ter) (see Appendix 3). Note – PM2 will NOT be used at moderate strength; PM2 will only be applied as a Supporting criterion.


If homozygotes are observed, the variant will meet BS2 (assuming 100% penetrance for an individual with 2 pathogenic variants in trans).
Gene: GATM (HGNC:4175)
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: GATM (HGNC:4175)
Evidence Code: PM3 — Very Strong
Modification Type: Strength
Follow SVI guidance for PM3 (
https://clinicalgenome.org/site/assets/files/3717/svi_proposal_for_pm3_criterion_-_version_1.pdf
).


Parental testing, or another appropriate molecular method (such as cloning each allele separately followed by sequencing), must have been performed in order to confirm that the variants are in trans if the patient is compound heterozygous.
Gene: GATM (HGNC:4175)
Evidence Code: PM3 — Strong
Modification Type: Strength
Follow SVI guidance for PM3 (
https://clinicalgenome.org/site/assets/files/3717/svi_proposal_for_pm3_criterion_-_version_1.pdf
).


Parental testing, or another appropriate molecular method (such as cloning each allele separately followed by sequencing), must have been performed in order to confirm that the variants are in trans if the patient is compound heterozygous.
Gene: GATM (HGNC:4175)
Evidence Code: PM3 — Moderate
Modification Type: None
Follow SVI guidance for PM3 (
https://clinicalgenome.org/site/assets/files/3717/svi_proposal_for_pm3_criterion_-_version_1.pdf
).


Parental testing, or another appropriate molecular method (such as cloning each allele separately followed by sequencing), must have been performed in order to confirm that the variants are in trans if the patient is compound heterozygous.
Gene: GATM (HGNC:4175)
Evidence Code: PM3 — Supporting
Modification Type: Strength
Follow SVI guidance for PM3 (
https://clinicalgenome.org/site/assets/files/3717/svi_proposal_for_pm3_criterion_-_version_1.pdf
).


Parental testing, or another appropriate molecular method (such as cloning each allele separately followed by sequencing), must have been performed in order to confirm that the variants are in trans if the patient is compound heterozygous.
Gene: GATM (HGNC:4175)
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: GATM (HGNC:4175)
Evidence Code: PM4 — Moderate
Modification Type: None
CCDS VCEP notes: Stop loss variants in GATM have not been reported, as far as we are aware. 


GATM specifications: Use this rule “as is” for in frame deletions and insertions of 2 or more amino acids, but downgrade to PM4_Supporting for single amino acid deletions and insertions.
Gene: GATM (HGNC:4175)
Evidence Code: PM4 — Supporting
Modification Type: Strength
Downgrade to PM4_Supporting for in frame deletion/insertion of a single amino acid.
Gene: GATM (HGNC:4175)
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: GATM (HGNC:4175)
Evidence Code: PM5 — Moderate
Modification Type: None
If the pathogenicity of another missense change at the same amino acid residue is unknown, determine its pathogenicity using these specifications in order to determine if this criterion can be used. If the variant is pathogenic, use PM5. If the variant is likely pathogenic, use PM5_Supporting.
Gene: GATM (HGNC:4175)
Evidence Code: PM5 — Supporting
Modification Type: Strength
Missense change at an amino acid residue where a different missense change determined to be likely pathogenic has been seen before.
Gene: GATM (HGNC:4175)
Evidence Code: PM6 — Original ACMG Summary
Assumed de novo, but without confirmation of paternity and maternity.
Gene: GATM (HGNC:4175)
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: GATM (HGNC:4175)
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: GATM (HGNC:4175)
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: GATM (HGNC:4175)
Evidence Code: PP3 — Moderate
Modification Type: None
Non-canonical splice site variant predicted to be more deleterious, by SpliceAI and varSEAK, than a previously observed pathogenic variant at the same nucleotide.
Gene: GATM (HGNC:4175)
Evidence Code: PP3 — Supporting
Modification Type: None
REVEL score >0.75 for missense variants.


In frame deletion or insertion predicted deleterious by PROVEAN and MutationTaster.


Predicted impact on splicing by SpliceAI and varSEAK. GATM specifications:


For missense changes, those with a REVEL score more than 0.75 will meet PP3.


For in frame insertions and deletions, use PROVEAN and Mutation Taster. Results must be consistent to count.


For non-canonical splice site variants (e.g., +3, -3), use SpliceAI ((
https://spliceailookup.broadinstitute.org/
 ) and varSEAK (
https://varseak.bio/
). Results must be consistent to apply this criterion.


For SpliceAI, any donor loss or acceptor loss with a score >0.5. For varSEAK, any variant with splicing class 4 or 5. Evidence for creation of a cryptic splice site should also be assessed.


Do not apply this rule for canonical splice site changes meeting PVS1.
Gene: GATM (HGNC:4175)
Evidence Code: PP4 — Original ACMG Summary
Patient’s phenotype or family history is highly specific for a disease with a single genetic etiology.
Gene: GATM (HGNC:4175)
Evidence Code: PP4 — Strong
Modification Type: Disease-specific
4 or more points based on any combination of the following. Two or more data types are required to meet Strong:
• Low urine guanidinoacetate with or without low or low normal creatine (1 point)
• Low plasma guanidinoacetate with or without low or low normal creatine (2 points)
• Significantly decreased creatine peak in brain magnetic resonance spectroscopy (3 points)
• AGAT enzyme activity <5% of normal (3 points)


* Variant must meet PM2_Supporting for PP4 to apply at any strength.
* For PP4 to be applied at strong, full GATM gene sequencing, including all coding exons and intron/exon boundaries, must have been carried out. If not, consider downgrading.
Gene: GATM (HGNC:4175)
Evidence Code: PP4 — Moderate
Modification Type: Strength
3 points based on any combination of the following. Two or more data types are recommended to reach moderate:
• Low urine guanidinoacetate with or without low or low normal creatine (1 point)
• Low plasma guanidinoacetate with or without low or low normal creatine (2 points)
• Significantly decreased creatine peak in brain magnetic resonance spectroscopy (3 points)
• AGAT enzyme activity <5% of normal (3 points)


Variant must meet PM2_Supporting for PP4 to apply at any strength.
Gene: GATM (HGNC:4175)
Evidence Code: PP4 — Supporting
Modification Type: Disease-specific
1-2 points based on:
• Low urine guanidinoacetate with or without low or low normal creatine (1 point)
• Low plasma guanidinoacetate with or without low or low normal creatine (2 points)
Variant must meet PM2_Supporting for PP4 to apply at any strength.
Gene: GATM (HGNC:4175)
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: GATM (HGNC:4175)
Evidence Code: BA1 — Original ACMG Summary
Allele frequency is above 5% in Exome Sequencing Project, 1000 Genomes or Exome Aggregation Consortium.