Evidence Repository
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.2639-17G>T

CA163513

140763 (ClinVar)

Gene: ATM
Condition: hereditary breast cancer
Inheritance Mode: Autosomal dominant inheritance
Link to MONDO
UUID: 12e51ac3-f131-4b31-8659-d7e9bb1ed185

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
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
NM_000051.4(ATM):c.2639-17G>T

Benign

Met criteria codes 3
BP4 BA1 BP2_Strong
Not Met criteria codes 4
BS1 BP7 PP3 PM2

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 1.1

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.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.
Met criteria codes
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).
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).
Not Met criteria codes
BS1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BP7
This variant is not considered deep intronic (beyond +20 or beyond -40).
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
Approved on: 2022-03-09
Published on: 2022-07-11
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