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 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.6116A>T (p.Glu2039Val)

CA16616706

417621 (ClinVar)

Gene: ATM
Condition: ATM-related cancer predisposition
Inheritance Mode: Autosomal dominant inheritance
Link to MONDO
UUID: 25a27723-e7f0-4cd2-b539-c701894e6cd6
Approved on: 2024-11-26
Published on: 2025-01-13

HGVS expressions

NM_000051.4:c.6116A>T
NM_000051.4(ATM):c.6116A>T (p.Glu2039Val)
NC_000011.10:g.108316031A>T
CM000673.2:g.108316031A>T
NC_000011.9:g.108186758A>T
CM000673.1:g.108186758A>T
NC_000011.8:g.107691968A>T
NG_009830.1:g.98200A>T
NG_054724.1:g.158802T>A
ENST00000452508.7:c.6116A>T
ENST00000713593.1:c.*5587A>T
ENST00000278616.9:c.6116A>T
ENST00000525056.2:n.535A>T
ENST00000682286.1:n.873A>T
ENST00000682302.1:n.534A>T
ENST00000683174.1:n.7600A>T
ENST00000683524.1:n.1340A>T
ENST00000684152.1:n.1830A>T
ENST00000527805.6:c.*1180A>T
ENST00000675595.1:c.*1180A>T
ENST00000675843.1:c.6116A>T
ENST00000278616.8:c.6116A>T
ENST00000452508.6:c.6116A>T
ENST00000524792.5:n.2331A>T
ENST00000525729.5:c.641-6960T>A
ENST00000532765.1:n.433A>T
ENST00000533690.5:n.1520A>T
NM_000051.3:c.6116A>T
NM_001330368.1:c.641-6960T>A
NM_001351110.1:c.*39-6960T>A
NM_001351834.1:c.6116A>T
NM_001330368.2:c.641-6960T>A
NM_001351110.2:c.*39-6960T>A
NM_001351834.2:c.6116A>T
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Uncertain Significance

Met criteria codes 2
PM2_Supporting PM3_Supporting
Not Met criteria codes 2
BP4 PP3

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.6116A>T variant in ATM is a missense variant predicted to cause substitution of glutamic acid by valine at amino acid 2039 (p.Glu2039Val). This variant has been detected in at least one individual with Ataxia-Telangiectasia (PMID: 26896183). This variant is absent from gnomAD v2.1.1. The computational predictor REVEL gives a score of 0.429, which is neither above nor below the thresholds predicting a damaging or benign impact on ATM function. In summary, this variant meets criteria to be classified as a variant of uncertain significance 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_Supporting, PM2_Supporting)
Met criteria codes
PM2_Supporting
This variant is absent from gnomAD v2.1.1.
PM3_Supporting
1 pt. PM3_supporting: This variant has been detected in at least one individual with Ataxia-Telangiectasia (PMID: 26896183).
Not Met criteria codes
BP4
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PP3
The computational predictor, Revel, gives a score of 0.429, which is neither above nor below the thresholds predicting a damaging or benign impact on ATM function.
Curation History
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