Evidence Repository - Clinical Genome Resources

The ClinGen Evidence Repository is an FDA-recognized human genetic variant database containing expert-curated assertions regarding variants' pathogenicity and supporting evidence summaries. [Disclaimer]

Link to SEPIO compliant JSON-LD document

Variant: NM_000051.3(ATM):c.3118A>G (p.Met1040Val)

CA151920

3027 (ClinVar)

Gene: ATM

Condition: hereditary breast cancer

Inheritance Mode: Autosomal dominant inheritance

Link to MONDO

UUID: 26ac1fa7-faca-44e7-9ae0-cb81579c10ae

Approved on: 2022-03-09

Published on: 2022-07-11

HGVS expressions

NM_000051.3:c.3118A>G

NM_000051.3(ATM):c.3118A>G (p.Met1040Val)

NC_000011.10:g.108272572A>G

CM000673.2:g.108272572A>G

NC_000011.9:g.108143299A>G

CM000673.1:g.108143299A>G

NC_000011.8:g.107648509A>G

NG_009830.1:g.54741A>G

ENST00000278616.9:c.3118A>G

ENST00000683174.1:n.3268A>G

ENST00000527805.6:c.3118A>G

ENST00000675595.1:c.2953A>G

ENST00000675843.1:c.3118A>G

ENST00000278616.8:c.3118A>G

ENST00000452508.6:c.3118A>G

ENST00000527805.5:c.3118A>G

NM_001351834.1:c.3118A>G

NM_001351834.2:c.3118A>G

NM_000051.4:c.3118A>G

NM_000051.4(ATM):c.3118A>G (p.Met1040Val)

Benign

BP2_Strong BP4 BA1

PM2 BS1

Evidence Links 0

Expert Panel

Hereditary Breast, Ovarian and Pancreatic Cancer VCEP

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 1.1

PDF

Criteria Specification Approval History

Criteria Specifications for this VCEP

Evidence submitted by expert panel

Hereditary Breast, Ovarian and Pancreatic Cancer VCEP

The ATM c.3118A>G (p.Met1040Val) variant has a GnomAD (v2.1.1) filtering allele frequency of 4.2% (AFR) which is above the ATM BA1 threshold of 0.5% (BA1). This variant has been observed in a homozygous state in multiple individuals without Ataxia-Telangiectasia (BP2_Strong, GTR Lab IDs: 500031, 61756). In silico protein predictors (BayesDel, score:-0.45, AGVGD, Class C0) predict that this alteration is not deleterious (BP4). In summary, this variant meets criteria to be classified as benign. ACMG/AMP criteria applied, as specified by the HBOP Variant Curation Expert Panel.

BP2_Strong

This variant has been observed in a homozygous state in multiple individuals without Ataxia-Telangiectasia (BP2_Strong, GTR Lab IDs: 500031, 61756).

BP4

In silico protein predictors (BayesDel, score:-0.45, AGVGD, Class C0) predict that this alteration is not deleterious (BP4).

BA1

This variant has a GnomAD (v2.1.1) filtering allele frequency of 4.2% (AFR) which is above the ATM BA1 threshold of 0.5% (BA1).

PM2

No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline

BS1

No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline

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