Evidence Repository - GenboreeKB

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.2639-17G>T

CA163513

140763 (ClinVar)

Gene: ATM (HGNC:472)

Condition: ATM-related cancer predisposition (MONDO:0700270)

Inheritance Mode: Autosomal dominant inheritance

UUID: 12e51ac3-f131-4b31-8659-d7e9bb1ed185

Approved on: 2022-03-09

Published on: 2025-09-15

HGVS expressions

NM_000051.3:c.2639-17G>T

NM_000051.3(ATM):c.2639-17G>T

NC_000011.10:g.108268393G>T

CM000673.2:g.108268393G>T

NC_000011.9:g.108139120G>T

CM000673.1:g.108139120G>T

NC_000011.8:g.107644330G>T

NG_009830.1:g.50562G>T

ENST00000452508.7:c.2639-17G>T

ENST00000713593.1:c.*2110-17G>T

ENST00000278616.9:c.2639-17G>T

ENST00000682516.1:n.2772+1051G>T

ENST00000683174.1:n.2789-17G>T

ENST00000684037.1:c.*1573+1051G>T

ENST00000527805.6:c.2639-17G>T

ENST00000675595.1:c.2474-17G>T

ENST00000675843.1:c.2639-17G>T

ENST00000278616.8:c.2639-17G>T

ENST00000452508.6:c.2639-17G>T

ENST00000527805.5:c.2639-17G>T

NM_001351834.1:c.2639-17G>T

NM_001351834.2:c.2639-17G>T

NM_000051.4:c.2639-17G>T

Benign

BA1 BP2_Strong BP4

BP7 BS1 PP3 PM2

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

Criteria Specification Approval History

Criteria Specifications for this VCEP

Evidence submitted by expert panel

Hereditary Breast, Ovarian and Pancreatic Cancer VCEP

The ATM c.2639-17G>T variant has a gnomAD v2.1.1 filtering allele frequency of 6.505% (African/African-American; exomes) which exceeds the ATM BA1 threshold of 0.50% (BA1). This variant has been observed in a homozygous state in multiple individuals without biallelic disease (BP2_Strong; GTR Lab ID: 61756). In silico splicing predictors (SpliceAI: AL 0.00/DL 0.00/AG 0.01/DG 0.00; MaxEntScan: +1.92% (wild type = 9.90, variant = 10.09)) find that this variant is unlikely to affect splicing (BP4). 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.

BA1

GnomAD v2.1.1 FAF 6.505% (African/African-American; exomes) exceeds ATM BA1 threshold of 0.50%.

BP2_Strong

This variant has been observed in a homozygous state in multiple individuals without biallelic disease (BP2_Strong; GTR Lab ID: 61756).

BP4

In silico splicing predictors (SpliceAI: AL 0.00/DL 0.00/AG 0.01/DG 0.00; MaxEntScan: +1.92% (wild type = 9.90, variant = 10.09)) find that this variant is unlikely to affect splicing (BP4).

BP7

This variant is not considered deep intronic (beyond +20 or beyond -40).

BS1

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

PP3

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

PM2

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

Curation History

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