Evidence Repository
The ClinGen Evidence Repository is an FDA-recognized human genetic variant database containing expert-curated assertions regarding variants' pathogenicity and supporting evidence summaries. [Disclaimer]
  • Gene label mismatch: ATM vs undefined
  • Gene obtained from curated document aligns with the Allele Registry but not with ClinVar data
  • Despite there being a valid 'cspec' property in the messages there's a discrepancy in message contents and CSPEC data: * Message Gene: ATM CSPEC Genes: [ 'ATM' ] * Message MONDOs: MONDO:0700270 CSPEC MONDO: [ 'MONDO:0016419', 'MONDO:0008840', 'MONDO:0018266' ]
  • No CSPEC computed assertion could be determined for this classification!

Variant: NM_000051.4(ATM):c.9103C>T (p.Leu3035Phe)

CA10579342

232110 (ClinVar)

Gene: ATM
Condition: ATM-related cancer predisposition
Inheritance Mode: Autosomal dominant inheritance
Link to MONDO
UUID: 5dd76349-0faa-43ca-bfac-46940d3ad107
Approved on: 2025-06-11
Published on: 2025-07-10

HGVS expressions

NM_000051.4:c.9103C>T
NM_000051.4(ATM):c.9103C>T (p.Leu3035Phe)
NC_000011.10:g.108365440C>T
CM000673.2:g.108365440C>T
NC_000011.9:g.108236167C>T
CM000673.1:g.108236167C>T
NC_000011.8:g.107741377C>T
NG_009830.1:g.147609C>T
NG_054724.1:g.109393G>A
ENST00000452508.7:c.9103C>T
ENST00000713593.1:c.*8574C>T
ENST00000278616.9:c.9103C>T
ENST00000638786.2:n.1801C>T
ENST00000682286.1:n.3860C>T
ENST00000682302.1:n.3521C>T
ENST00000682569.1:n.2450C>T
ENST00000683174.1:n.10587C>T
ENST00000683524.1:n.4327C>T
ENST00000684152.1:n.4519C>T
ENST00000684180.1:n.1577C>T
ENST00000684447.1:n.5596C>T
ENST00000527805.6:c.*4167C>T
ENST00000675595.1:c.*4238C>T
ENST00000675843.1:c.9103C>T
ENST00000278616.8:c.9103C>T
ENST00000452508.6:c.9103C>T
ENST00000524755.5:c.226+27768G>A
ENST00000524792.5:n.5318C>T
ENST00000525178.5:n.591C>T
ENST00000525729.5:c.640+20480G>A
ENST00000526725.1:n.272-25076G>A
ENST00000527181.1:n.442C>T
ENST00000527531.5:c.*2-9331G>A
ENST00000615746.4:c.*2-9331G>A
NM_000051.3:c.9103C>T
NM_001330368.1:c.640+20480G>A
NM_001351110.1:c.694+20480G>A
NM_001351834.1:c.9103C>T
NR_147053.2:n.1107-9331G>A
NM_001330368.2:c.640+20480G>A
NM_001351110.2:c.694+20480G>A
NM_001351834.2:c.9103C>T
NR_147053.3:n.1105-9331G>A
More

Likely Pathogenic

Met criteria codes 3
PP3 PM2_Supporting PM3_Strong

Evidence Links 0

Expert Panel

Criteria Specification Information

Criteria Specification: ClinGen Hereditary Breast, Ovarian and Pancreatic Cancer Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines for ATM Version 1.3.0

Criteria Specification Approval History
Criteria Specifications for this VCEP
Evidence submitted by expert panel
Hereditary Breast, Ovarian and Pancreatic Cancer VCEP
The c.9103C>T variant in ATM is a missense variant predicted to cause substitution of leucine by phenylalanine at amino acid 3035 (p.Leu3035Phe). This variant has been detected in at least two unrelated individuals with Ataxia-Telangiectasia (PMIDs: 16941484, 30549301). This variant is absent in gnomAD v4.1.0. The computational predictor REVEL gives a score of 0.963, which is above the threshold of 0.733, evidence that correlates with impact to ATM function. In summary, this variant meets criteria to be classified as pathogenic for autosomal dominant ATM-related cancer predisposition and autosomal recessive Ataxia-Telangiectasia based on the ACMG/AMP criteria applied as specified by the HBOP VCEP. (PM3_ Strong, PM2_Supporting, PP3)
Met criteria codes
PP3
The computational predictor REVEL gives a score of 0.963,which is above the threshold of ≥.733, evidence that correlates with impact to ATM function.
PM2_Supporting
This variant is absent in gnomAD v4
PM3_Strong
This Variant has been detected in at least 2 individuals with Ataxia-Telangiectasia (PMID: 16941484,30549301)
Curation History
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