owencqueen/cgbench_data huggingface dataset:
Gene: ATM (HGNC:795)
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: ATM (HGNC:795)
Evidence Code: PVS1 — Very Strong
Modification Type: Gene-specific,Strength
Use ATM PVS1 Decision Tree
Gene: ATM (HGNC:795)
Evidence Code: PVS1 — Strong
Modification Type: Gene-specific,Strength
Use ATM PVS1 Decision Tree.
Gene: ATM (HGNC:795)
Evidence Code: PVS1 — Moderate
Modification Type: Gene-specific,Strength
Use ATM PVS1 Decision Tree.
Gene: ATM (HGNC:795)
Evidence Code: PVS1 — Supporting
Modification Type: Gene-specific,Strength
Use ATM PVS1 Decision Tree
Gene: ATM (HGNC:795)
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: ATM (HGNC:795)
Evidence Code: PS1 — Strong
Modification Type: General recommendation
Use for protein changes as long as splicing is ruled-out for both alterations.
Gene: ATM (HGNC:795)
Evidence Code: PS1 — Moderate
Modification Type: Strength,General recommendation
Use for RNA changes as code PS1_RNA_Moderate if predictions or observations are similar or worse for the variant under consideration. Close matches must be VCEP approved LP/P variants.
Gene: ATM (HGNC:795)
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: ATM (HGNC:795)
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: ATM (HGNC:795)
Evidence Code: PS3 — Strong
Modification Type: Gene-specific
Do not use as strong.
Gene: ATM (HGNC:795)
Evidence Code: PS3 — Moderate
Modification Type: Gene-specific,Strength
Use when a variant fails to rescue both an ATM specifc feature (e.g. phosphorylation of ATM-specific targets) AND radiosensitivity.
Gene: ATM (HGNC:795)
Evidence Code: PS3 — Supporting
Modification Type: Gene-specific,Strength
Use when a variant fails to rescue an ATM specifc feature, only (e.g. phosphorylation of ATM-specific targets). Do not use for radiosensitivity-only as that is not a feature specific to ATM deficiency
Gene: ATM (HGNC:795)
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: ATM (HGNC:795)
Evidence Code: PS4 — Strong
Modification Type: General recommendation
Use for case control studies that reflect an OR ≥2, p≤.05 and lower 95% CI ≥1.5.
Gene: ATM (HGNC:795)
Evidence Code: PS4 — Moderate
Modification Type: Gene-specific,Disease-specific
Do not use for proband counting.
Gene: ATM (HGNC:795)
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: ATM (HGNC:795)
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: ATM (HGNC:795)
Evidence Code: PM2 — Supporting
Modification Type: Gene-specific,Strength
Frequency ≤.001% when N>1 in a large general population database (e.g. gnomAD 2.1.1)
Gene: ATM (HGNC:795)
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: ATM (HGNC:795)
Evidence Code: PM3 — Very Strong
Modification Type: Gene-specific,Disease-specific,Strength,General recommendation
Use ATM PM3/BP2 table.
Gene: ATM (HGNC:795)
Evidence Code: PM3 — Strong
Modification Type: Gene-specific,Disease-specific,Strength,General recommendation
Use ATM PM3/BP2 table.
Gene: ATM (HGNC:795)
Evidence Code: PM3 — Moderate
Modification Type: Gene-specific,Disease-specific,Strength,General recommendation
Use ATM PM3/BP2 table.
Gene: ATM (HGNC:795)
Evidence Code: PM3 — Supporting
Modification Type: Gene-specific,Disease-specific,Strength,General recommendation
Use ATM PM3/BP2 table
Gene: ATM (HGNC:795)
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: ATM (HGNC:795)
Evidence Code: PM4 — Moderate
Modification Type: Gene-specific,General recommendation
Use for stop-loss variants.
Gene: ATM (HGNC:795)
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: ATM (HGNC:795)
Evidence Code: PM5 — Supporting
Modification Type: Gene-specific,Strength
Use for genomic frameshift and truncating variants with PTC upstream of p.R3047. Do not use for splice or start-loss variants
Gene: ATM (HGNC:795)
Evidence Code: PM6 — Original ACMG Summary
Assumed de novo, but without confirmation of paternity and maternity.
Gene: ATM (HGNC:795)
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: ATM (HGNC:795)
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: ATM (HGNC:795)
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: ATM (HGNC:795)
Evidence Code: PP3 — Supporting
Protein: REVEL >.7333; RNA: multiple in silico predictors agree to a smilar effect
Gene: ATM (HGNC:795)
Evidence Code: PP4 — Original ACMG Summary
Patient’s phenotype or family history is highly specific for a disease with a single genetic etiology.
Gene: ATM (HGNC:795)
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: ATM (HGNC:795)
Evidence Code: BA1 — Original ACMG Summary
Allele frequency is above 5% in Exome Sequencing Project, 1000 Genomes or Exome Aggregation Consortium.
Gene: ATM (HGNC:795)
Evidence Code: BA1 — Stand Alone
Filtering Allele Frequency >.5%.
Gene: ATM (HGNC:795)
Evidence Code: BS1 — Original ACMG Summary
Allele frequency is greater than expected for disorder.
Gene: ATM (HGNC:795)
Evidence Code: BS1 — Strong
Filtering Allele Frequency >.05%.
Gene: ATM (HGNC:795)
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: ATM (HGNC:795)
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: ATM (HGNC:795)
Evidence Code: BS3 — Moderate
Modification Type: Gene-specific,Disease-specific,Strength,General Recommendation
Use when a variant rescues both an ATM specifc feature (e.g. phosphorylation of ATM-specific targets) AND radiosensitivity.
Gene: ATM (HGNC:795)
Evidence Code: BS3 — Supporting
Modification Type: Gene-specific,Disease-specific,Strength,General Recommendation
Use when a variant rescues EITHER an ATM specifc feature OR rescues radiosensitivity.
Gene: ATM (HGNC:795)
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: ATM (HGNC:795)
Evidence Code: BP1 — Original ACMG Summary
Missense variant in a gene for which primarily truncating variants are known to cause disease.
Gene: ATM (HGNC:795)
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: ATM (HGNC:795)
Evidence Code: BP2 — Strong
Modification Type: Gene-specific,Disease-specific,Strength,General recommendation
Use ATM PM3/BP2 table.
Gene: ATM (HGNC:795)
Evidence Code: BP2 — Moderate
Modification Type: Gene-specific,Disease-specific,Strength,General recommendation
Use ATM PM3/BP2 table.
Gene: ATM (HGNC:795)
Evidence Code: BP2 — Supporting
Modification Type: Gene-specific,Disease-specific,Strength,General recommendation
Use ATM PM3/BP2 table
Gene: ATM (HGNC:795)
Evidence Code: BP3 — Original ACMG Summary
In frame-deletions/insertions in a repetitive region without a known function.
Gene: ATM (HGNC:795)
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: ATM (HGNC:795)
Evidence Code: BP5 — Original ACMG Summary
Variant found in a case with an alternate molecular basis for disease.
Gene: ATM (HGNC:795)
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: ATM (HGNC:795)
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: ATM (HGNC:795)
Evidence Code: BP7 — Strong
Modification Type: General recommendation
Can be considered for BP7_O with curator discretion of quality.
Gene: ATM (HGNC:795)
Evidence Code: BP7 — Moderate
Modification Type: General recommendation
Can be considered for BP7_O with curator discretion of quality.
Gene: ATM (HGNC:795)
Evidence Code: BP7 — Supporting
Modification Type: General recommendation
Can be considered for BP7_O with curator discretion of quality; Use for synonymous and deep intronic variants defined as further than (but not including) +7 and further than (but not including) -40 at donor and acceptor sites, respectively