The ClinGen Evidence Repository is an FDA-recognized human genetic variant database containing expert-curated assertions regarding variants' pathogenicity and supporting evidence summaries. [Disclaimer]
  • Gene label mismatch: ATM vs undefined
  • Gene obtained from curated document aligns with the Allele Registry but not with ClinVar data
  • No CSPEC computed assertion could be determined for this classification!


Variant: NM_000051.4(ATM):c.4158dup (p.Lys1387Ter)

CA2695214771

3148196 (ClinVar)

Gene: ATM (HGNC:472)
Condition: ATM-related cancer predisposition (MONDO:0700270)
Inheritance Mode: Autosomal dominant inheritance
UUID: 347e9855-bece-4a30-ade8-c2f88b27b0ef
Approved on: 2025-06-19
Published on: 2026-04-10

HGVS expressions

NM_000051.4(ATM):c.4158dup (p.Lys1387Ter)
NM_000051.4:c.4158dup
NC_000011.10:g.108289025dup
CM000673.2:g.108289025dup
NC_000011.9:g.108159752dup
CM000673.1:g.108159752dup
NC_000011.8:g.107664962dup
NG_009830.1:g.71194dup
ENST00000452508.7:c.4158dup
ENST00000713593.1:c.*3629dup
ENST00000278616.9:c.4158dup
ENST00000533733.6:n.1421dup
ENST00000683174.1:n.4308dup
ENST00000527805.6:c.4158dup
ENST00000675595.1:c.3993dup
ENST00000675843.1:c.4158dup
ENST00000278616.8:c.4158dup
ENST00000452508.6:c.4158dup
ENST00000524792.5:n.373dup
ENST00000531525.2:c.165dup
ENST00000533733.5:n.587dup
NM_000051.3:c.4158dup
NM_001351834.1:c.4158dup
NM_001351834.2:c.4158dup
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Pathogenic

Met criteria codes 4
PM2_Supporting PVS1 PM5_Supporting PM3_Strong

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 1.3.0

Criteria Specification Approval History
Criteria Specifications for this VCEP
Evidence submitted by expert panel
Hereditary Breast, Ovarian and Pancreatic Cancer VCEP
The c.4158dup (p.Lys1387*) variant in ATM is a nonsense variant predicted to cause a premature stop codon in 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 has been detected in at least two unrelated individuals with Ataxia-Telangiectasia (PMID: 26896183). The highest minor allele frequency in gnomAD v4.1.0 is 0.00003381 (1/29576 alleles) in the Ashkenazi Jewish population; while this is higher than the HBOP VCEP threshold (≤0.00001) for PM2_Supporting, it is present in only one allele, meeting this criterion. In summary, this variant meets the criteria to be classified as pathogenic for autosomal dominant ATM-related cancer predisposition and autosomal recessive Ataxia-Telangiectasia based on the ACMG/AMP criteria applied as specified by the HBOP VCEP. (PVS1, PM5_Supporting, PM3_Strong, PM2_Supporting)
Met criteria codes
PM2_Supporting
The highest minor allele frequency in gnomAD v4.1.0 is 0.00003381 (1/29576 alleles) in Ashkenazi Jewish population, which is higher than the ClinGen HBOP VCEP threshold (>.001%, N=1) for PM2_Supporting, meeting this criterion (PM2_Supporting).
PVS1
The c.4158dup (p.Lys1387Ter) (NM_000051.4) variant in ATM is a nonsense variant predicted to cause a premature stop codon in biologically-relevant-exon leading to nonsense mediated decay (PVS1).
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).
PM3_Strong
This variant has been detected in at least 2 unrelated individuals with Ataxia-Telangiectasia (PMID: 26896183).
Curation History
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