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]

Variant: NM_000051.4(ATM):c.1066-6T>G

Curation Version - 1.1
Curation History
JSON LD for Version 1.1

CA151456

3038 (ClinVar)

Gene: ATM

Condition: hereditary breast cancer

Inheritance Mode: Autosomal dominant inheritance

Link to MONDO

UUID: bccd9f16-4086-4c14-8d78-04c52ad58630

Approved on: 2022-03-09

Published on: 2022-07-11

HGVS expressions

NM_000051.4:c.1066-6T>G

NM_000051.4(ATM):c.1066-6T>G

NC_000011.10:g.108248927T>G

CM000673.2:g.108248927T>G

NC_000011.9:g.108119654T>G

CM000673.1:g.108119654T>G

NC_000011.8:g.107624864T>G

NG_009830.1:g.31096T>G

ENST00000278616.9:c.1066-6T>G

ENST00000682516.1:n.1200-6T>G

ENST00000682956.1:n.1200-6T>G

ENST00000683174.1:n.1216-6T>G

ENST00000683605.1:n.561-6T>G

ENST00000684037.1:c.*1-6T>G

ENST00000684061.1:n.1200-6T>G

ENST00000684179.1:n.1035-6T>G

ENST00000527805.6:c.1066-6T>G

ENST00000675595.1:c.901-6T>G

ENST00000675843.1:c.1066-6T>G

ENST00000278616.8:c.1066-6T>G

ENST00000452508.6:c.1066-6T>G

ENST00000527805.5:c.1066-6T>G

NM_000051.3:c.1066-6T>G

NM_001351834.1:c.1066-6T>G

NM_001351834.2:c.1066-6T>G

Benign

BP2_Strong BS1

BP4 PM2 BA1

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.1066-6T>G variant has a GnomAD (v2.1.1) filtering allele frequency of 0.2081% (NFE) which is above the ATM BS1 threshold of .05% (BS1). In silico predictors (SpliceAI Acceptor Loss 0.62; MaxEntScan -2.49) are indeterminate about whether this variant affects splicing. This variant has been observed in a homozygous and compound heterozygous state (presumed) in multiple individuals without Ataxia-Telangiectasia (BP2_Strong, GTR Lab IDs: 61756, 26957, 500031). In summary, this variant meets criteria to be classified as benign based on the ACMG/AMP criteria applied as specified by the HBOP Variant Curation Expert Panel

BP2_Strong

This variant has been observed in a homozygous and compound heterozygous state (presumed) in multiple individuals without Ataxia-Telangiectasia (BP2_Strong, GTR Lab IDs: 61756, 26957, 500031).

BS1

This variant has a GnomAD (v2.1.1) filtering allele frequency of 0.2% (NFE) which is above the ATM BS1 threshold of 0.05% (BS1).

BP4

In silico predictors (SpliceAI Acceptor Loss 0.62; MaxEntScan -2.49) are indeterminate about whether this variant affects splicing.

PM2

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

BA1

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

Curation History

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