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 obtained from curated document aligns with the Allele Registry but not with ClinVar data
  • Despite there being a valid 'cspec' property in the messages there's a discrepancy in message contents and CSPEC data: * Message Gene: ATM CSPEC Genes: [ 'ATM' ] * Message MONDOs: MONDO:0700270 CSPEC MONDO: [ 'MONDO:0016419', 'MONDO:0008840', 'MONDO:0018266' ]
  • No CSPEC computed assertion could be determined for this classification!


Variant: NM_000051.4(ATM):c.1402_1403del (p.Lys468fs)

CA163840

140889 (ClinVar)

Gene: ATM
Condition: ATM-related cancer predisposition
Inheritance Mode: Autosomal dominant inheritance
UUID: ac5107da-45ba-4894-adb4-391957684b08
Approved on: 2024-11-26
Published on: 2025-01-13

HGVS expressions

NM_000051.4:c.1402_1403del
NM_000051.4(ATM):c.1402_1403del (p.Lys468fs)
NC_000011.10:g.108250867_108250868del
CM000673.2:g.108250867_108250868del
NC_000011.9:g.108121594_108121595del
CM000673.1:g.108121594_108121595del
NC_000011.8:g.107626804_107626805del
NG_009830.1:g.33036_33037del
ENST00000452508.7:c.1402_1403del
ENST00000713593.1:c.*873_*874del
ENST00000278616.9:c.1402_1403del
ENST00000682516.1:n.1536_1537del
ENST00000682956.1:n.1536_1537del
ENST00000683174.1:n.1552_1553del
ENST00000683605.1:n.897_898del
ENST00000684037.1:c.*337_*338del
ENST00000684061.1:n.1536_1537del
ENST00000684179.1:n.1371_1372del
ENST00000527805.6:c.1402_1403del
ENST00000675595.1:c.1237_1238del
ENST00000675843.1:c.1402_1403del
ENST00000278616.8:c.1402_1403del
ENST00000452508.6:c.1402_1403del
ENST00000527805.5:c.1402_1403del
NM_000051.3:c.1402_1403del
NM_001351834.1:c.1402_1403del
NM_001351834.2:c.1402_1403del
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Pathogenic

Met criteria codes 3
PVS1 PM5_Supporting PM3_Strong
Not Met criteria codes 1
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 1.3.0

Criteria Specification Approval History
Criteria Specifications for this VCEP
Evidence submitted by expert panel
Hereditary Breast, Ovarian and Pancreatic Cancer VCEP
The c.1402_1403del (p.Lys468Glufs*18) variant in ATM is a frameshift variant in a biologically-relevant-exon predicted to cause a premature stop codon 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-terminus 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 3 individuals with Ataxia-Telangiectasia (PMID: 23807571, 26896183, 31691010). The highest population minor allele frequency in gnomAD v2.1.1 is 0.0003 in the East Asian population (PM2_Supporting, BS1, and BA1 are not met). In summary, this variant meets 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 Variant Curation Expert Panel. (PVS1, PM5_Supporting, PM3_Strong)
Met criteria codes
PVS1
This variant in ATM is a nonsense variant predicted to cause a premature stop codon leading to nonsense mediated decay in a gene in which loss-of-function is an established disease mechanism.
PM5_Supporting
This alteration results in a termination codon upstream of the most C-terminus pathogenic alteration (p.Arg3047*).
PM3_Strong
This variant has been detected in 3 atleast individuals with Ataxia-Telangiectasia.(PMID:26896183,31691010,23807571)
Not Met criteria codes
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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