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Variant: NM_000051.4(ATM):c.3102T>G (p.Tyr1034Ter)

CA382515111

556315 (ClinVar)

Gene: ATM
Condition: hereditary breast cancer
Inheritance Mode: Autosomal dominant inheritance
UUID: 756acc7f-cc37-4f6f-92d4-f2a193bcab5b

HGVS expressions

NM_000051.4:c.3102T>G
NM_000051.4(ATM):c.3102T>G (p.Tyr1034Ter)
NC_000011.10:g.108272556T>G
CM000673.2:g.108272556T>G
NC_000011.9:g.108143283T>G
CM000673.1:g.108143283T>G
NC_000011.8:g.107648493T>G
NG_009830.1:g.54725T>G
ENST00000452508.7:c.3102T>G
ENST00000713593.1:c.*2573T>G
ENST00000278616.9:c.3102T>G
ENST00000683174.1:n.3252T>G
ENST00000527805.6:c.3102T>G
ENST00000675595.1:c.2937T>G
ENST00000675843.1:c.3102T>G
ENST00000278616.8:c.3102T>G
ENST00000452508.6:c.3102T>G
ENST00000527805.5:c.3102T>G
NM_000051.3:c.3102T>G
NM_001351834.1:c.3102T>G
NM_001351834.2:c.3102T>G

Pathogenic

Met criteria codes 4
PM3_Strong PM2_Supporting PM5_Supporting PVS1

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 1.2.0

Criteria Specification Approval History
Criteria Specifications for this VCEP
Evidence submitted by expert panel
Hereditary Breast, Ovarian and Pancreatic Cancer VCEP
The c.3102T>G (p.Tyr1034Ter) variant in ATM is a nonsense variant predicted to cause a premature stop codon in a biologically-relevant-exon leading to nonsense mediated decay in a gene in which loss-of-function is an established disease mechanism. This alteration results in a termination codon upstream of the most C-terminal pathogenic alteration (ATM p.Arg3047*), as classified by the HBOP VCEP, and is expected to be more deleterious. This variant is absent from gnomAD v.2.1.1. This variant has been detected in at least 4 individuals with Ataxia-Telangiectasia (PMID: 26896183, 18321536, 33547824). In summary, this variant meets criteria to be classified as pathogenic for autosomal dominant hereditary breast cancer and autosomal recessive Ataxia-Telangiectasia based on the ACMG/AMP criteria applied, as specified by the HBOP VCEP. (PVS1, PM3_strong, PM2_Supporting , PM5_Supporting)
Met criteria codes
PM3_Strong
This variant has been detected in 4 unrelated individuals with Ataxia-Telangiectasia (PM3_strong; PMID: 26896183, 18321536, 33547824).
PM2_Supporting
This variant is absent from gnomAD v.2.1.1 (PM2_Supporting).
PM5_Supporting
This alteration results in a termination codon upstream of the most C-terminal pathogenic alteration (ATM p.Arg3047*), as classified by the HBOP VCEP, and is expected to be more deleterious (PM5_Supporting).
PVS1
This variant is predicted to create an NMD-escaping transcript resulting in a loss of part of the HEAT repeat domain (PVS1).
Approved on: 2024-01-25
Published on: 2024-02-14
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