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.7661A>G (p.His2554Arg)

CA501111

846136 (ClinVar)

Gene: ATM
Condition: ATM-related cancer predisposition
Inheritance Mode: Autosomal dominant inheritance
UUID: 8c9e005f-242f-45b8-8936-938bcafdca9e
Approved on: 2024-11-26
Published on: 2025-01-13

HGVS expressions

NM_000051.4:c.7661A>G
NM_000051.4(ATM):c.7661A>G (p.His2554Arg)
NC_000011.10:g.108331910A>G
CM000673.2:g.108331910A>G
NC_000011.9:g.108202637A>G
CM000673.1:g.108202637A>G
NC_000011.8:g.107707847A>G
NG_009830.1:g.114079A>G
NG_054724.1:g.142923T>C
ENST00000452508.7:c.7661A>G
ENST00000713593.1:c.*7132A>G
ENST00000278616.9:c.7661A>G
ENST00000525056.2:n.2080A>G
ENST00000525537.3:n.618A>G
ENST00000638786.2:n.498A>G
ENST00000682286.1:n.2418A>G
ENST00000682302.1:n.2079A>G
ENST00000683174.1:n.9145A>G
ENST00000683524.1:n.2885A>G
ENST00000684152.1:n.3343+353A>G
ENST00000684447.1:n.2445A>G
ENST00000527805.6:c.*2725A>G
ENST00000675595.1:c.*2796A>G
ENST00000675843.1:c.7661A>G
ENST00000278616.8:c.7661A>G
ENST00000452508.6:c.7661A>G
ENST00000524755.5:c.300-343T>C
ENST00000524792.5:n.3876A>G
ENST00000525729.5:c.641-22839T>C
ENST00000527531.5:c.*1270-343T>C
ENST00000533690.5:n.3065A>G
ENST00000615746.4:c.*1270-343T>C
NM_000051.3:c.7661A>G
NM_001330368.1:c.641-22839T>C
NM_001351110.1:c.*38+3310T>C
NM_001351834.1:c.7661A>G
NR_147053.2:n.2375-343T>C
NM_001330368.2:c.641-22839T>C
NM_001351110.2:c.*38+3310T>C
NM_001351834.2:c.7661A>G
NR_147053.3:n.2373-343T>C
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Uncertain Significance

Met criteria codes 3
PM3 PM2_Supporting 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.7661A>G variant in ATM is a missense variant predicted to cause substitution of histidine by arginine at amino acid 2554 (p.His2554Arg). This variant has been detected in at least 1 individual with Ataxia-Telangiectasia (PMID: 26896183). This variant is absent from gnomAD v.2.1.1. The computational predictor REVEL gives a score of 0.884, which is above the threshold of 0.733, evidence that correlates with impact to ATM function. In summary, this variant meets the 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, PM2_Supporting, PP3)
Met criteria codes
PM3
This variant has been detected in at least 1 individual with Ataxia-Telangiectasia (PMID: 26896183). 2 POINTS: one AT patient with second pathogenic variant (c.3802delG, p.Val1268Ter). Phenotype Confident, phase unknown.
PM2_Supporting
PP3
The computational predictor gives a score of 0.884, which is above the threshold of 0.733, evidence that correlates with impact to ATM function (PP3).
Curation History
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