owencqueen/cgbench_data huggingface dataset:
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. Use ATM PS1 Splicing table for splicing variants with similar predictions or observations of splice defect.
Gene: ATM (HGNC:795)
Evidence Code: PS1 — Moderate
Modification Type: General recommendation,Strength
Use for protein changes as long as splicing is ruled-out for both alterations. Use ATM PS1 Splicing table for splicing variants with similar predictions or observations of splice defect.
Gene: ATM (HGNC:795)
Evidence Code: PS4 — Strong
Modification Type: General recommendation
Case-control studies; p-value ≤.05 AND (Odds ratio, hazard ratio, or relative risk  ≥2 OR lower 95% CI ≥1.5).
Gene: ATM (HGNC:795)
Evidence Code: PS4 — Moderate
Modification Type: Disease-specific,Gene-specific
Do not use for proband counting.
Gene: ATM (HGNC:795)
Evidence Code: PM2 — Supporting
Modification Type: Gene-specific,Strength
Frequency ≤.001% if n=1 in a single sub population, that is sufficiently rare and PM2_supporting would apply. n>1 in one or multiple subpopulations would not be considered rare and PM2_supporting would not apply
Gene: ATM (HGNC:795)
Evidence Code: PM3 — Very Strong
Modification Type: Disease-specific,General recommendation,Gene-specific,Strength
Use ATM PM3/BP2 table.
Gene: ATM (HGNC:795)
Evidence Code: PM3 — Strong
Modification Type: Disease-specific,General recommendation,Gene-specific,Strength
Use ATM PM3/BP2 table.
Gene: ATM (HGNC:795)
Evidence Code: PM3 — Moderate
Modification Type: Disease-specific,General recommendation,Gene-specific,Strength
Use ATM PM3/BP2 table.
Gene: ATM (HGNC:795)
Evidence Code: PM3 — Supporting
Modification Type: Disease-specific,General recommendation,Gene-specific,Strength
Use ATM PM3/BP2 table
Gene: ATM (HGNC:795)
Evidence Code: PM4 — Moderate
Modification Type: General recommendation,Gene-specific
Use for stop-loss variants.
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. Apply also to splice variants as PM5_supporting for splice variants can only be applied for variants premature termination codons upstream of p.Arg3047 where PVS1_VS(RNA) is applied based on high quality observed splicing impact and must be NMD prone. Do not use for start-loss variants
Gene: ATM (HGNC:795)
Evidence Code: PP3 — Supporting
Modification Type: Gene-specific
Protein: REVEL >.7333; RNA: At least one well-established in silico predictor (e.g. SpliceAI) shows impact on splicing
Gene: ATM (HGNC:795)
Evidence Code: BA1 — Stand Alone
Modification Type: Disease-specific
Filtering Allele Frequency >.5%.
Gene: ATM (HGNC:795)
Evidence Code: BS1 — Strong
Modification Type: Disease-specific
Filtering Allele Frequency >.05%.
Gene: ATM (HGNC:795)
Evidence Code: BS3 — Moderate
Modification Type: Disease-specific,Gene-specific,Strength
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: Disease-specific,Gene-specific,Strength
Use when a variant rescues EITHER an ATM specifc feature OR rescues radiosensitivity.
Gene: ATM (HGNC:795)
Evidence Code: BP2 — Strong
Modification Type: Disease-specific,General recommendation,Gene-specific,Strength
Use ATM PM3/BP2 table.
Gene: ATM (HGNC:795)
Evidence Code: BP2 — Moderate
Modification Type: Disease-specific,General recommendation,Gene-specific,Strength
Use ATM PM3/BP2 table.
Gene: ATM (HGNC:795)
Evidence Code: BP2 — Supporting
Modification Type: Disease-specific,General recommendation,Gene-specific,Strength
Use ATM PM3/BP2 table
Gene: ATM (HGNC:795)
Evidence Code: BP4 — Supporting
Modification Type: General recommendation
Protein
 Analysis: Metapredictor REVEL score ≤.249


RNA: At least one well-established in silico predictor (e.g. SpliceAI) shows impact on splicing 


NOTE: Splice analysis needs to be considered for all variant types (including missense, frameshift, nonsense, etc. as any variant has the potential to impact splicing which may preclude any expected protein effects) 


NOTE: BP4 for splice predictions may not be applied in conjunction with BP7_Variable(RNA) (a lack of observed RNA defect) Use caution in applying the wrong type of computational evidence (protein vs. RNA) towards the cumulative body of evidence for the opposite mechanism.
Gene: ATM (HGNC:795)
Evidence Code: BP7 — Strong
Modification Type: General recommendation
Can be considered for BP7_(RNA) with curator discretion of quality.
Gene: ATM (HGNC:795)
Evidence Code: BP7 — Moderate
Modification Type: General recommendation
Can be considered for BP7_(RNA) with curator discretion of quality.
Gene: ATM (HGNC:795)
Evidence Code: BP7 — Supporting
Modification Type: General recommendation
Can be considered for BP7_(RNA) 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