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_000051.3(ATM):c.1607+1G>T

Curation Version - 1.3
Curation History
JSON LD for Version 1.3

CA348209

220555 (ClinVar)

Gene: ATM

Condition: hereditary breast cancer

Inheritance Mode: Autosomal dominant inheritance

Link to MONDO

UUID: e356a4a5-315c-40ed-834e-1c861ad5a22a

Approved on: 2022-03-16

Published on: 2022-07-12

HGVS expressions

NM_000051.3:c.1607+1G>T

NM_000051.3(ATM):c.1607+1G>T

NC_000011.10:g.108251073G>T

CM000673.2:g.108251073G>T

NC_000011.9:g.108121800G>T

CM000673.1:g.108121800G>T

NC_000011.8:g.107627010G>T

NG_009830.1:g.33242G>T

ENST00000278616.9:c.1607+1G>T

ENST00000682516.1:n.1741+1G>T

ENST00000682956.1:n.1742G>T

ENST00000683174.1:n.1757+1G>T

ENST00000683605.1:n.1102+1G>T

ENST00000684037.1:c.*542+1G>T

ENST00000684061.1:n.1741+1G>T

ENST00000684179.1:n.1577G>T

ENST00000527805.6:c.1607+1G>T

ENST00000675595.1:c.1442+1G>T

ENST00000675843.1:c.1607+1G>T

ENST00000278616.8:c.1607+1G>T

ENST00000452508.6:c.1607+1G>T

ENST00000527805.5:c.1607+1G>T

NM_001351834.1:c.1607+1G>T

NM_001351834.2:c.1607+1G>T

NM_000051.4:c.1607+1G>T

NM_000051.4(ATM):c.1607+1G>T

Pathogenic

PM3_Very Strong PVS1_Strong PM2_Supporting

BA1 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.1607+1G>T canonical splice variant is predicted to result in a truncated protein that disrupts a critical functional domain (PVS1_Strong). This variant has been observed in a homozygous and compound heterozygous state in multiple individuals with Ataxia-Telangiectasia (PMIDs: 10330348, 1712434, 9450906, 19691550, PM3_VeryStrong). This variant has a GnomAD (v2.1.1) allele frequency of 0.0009% (NFE) which is below the ATM PM2 threshold of 0.001% (PM2_Supporting). In summary, this variant meets criteria to be classified as pathogenic. ACMG/AMP criteria applied, as specified by the HBOP Variant Curation Expert Panel.

PM3_Very Strong

This variant has been observed in a homozygous and/or compound heterozygous state (presumed and/or confirmed) in one/multiple individuals with Ataxia-Telangiectasia (PMIDs: 10330348, 1712434, 9450906) (8 points)

PVS1_Strong

The c.1607+1G>T canonical splice variant is predicted to result in a truncated protein that disrupts a critical functional domain (PVS1_Strong).

PM2_Supporting

This variant has a GnomAD (v2.1.1) allele frequency of 0.0009% (NFE) which is below the ATM PM2 threshold of 0.001% (PM2_Supporting).

BA1

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

Curation History

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