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_000051.4(ATM):c.824del (p.Ser274_Leu275insTer)

CA349767

220121 (ClinVar)

Gene: ATM
Condition: hereditary breast cancer
Inheritance Mode: Autosomal dominant inheritance
UUID: 1484b53f-94c3-4f9f-8f34-5092caaa64b1
Approved on: 2024-01-25
Published on: 2024-02-14

HGVS expressions

NM_000051.4:c.824del
NM_000051.4(ATM):c.824del (p.Ser274_Leu275insTer)
NC_000011.10:g.108244949del
CM000673.2:g.108244949del
NC_000011.9:g.108115676del
CM000673.1:g.108115676del
NC_000011.8:g.107620886del
NG_009830.1:g.27118del
ENST00000452508.7:c.824del
ENST00000713593.1:c.*295del
ENST00000278616.9:c.824del
ENST00000682430.1:n.923del
ENST00000682516.1:n.958del
ENST00000682956.1:n.958del
ENST00000683100.1:n.3171del
ENST00000683174.1:n.974del
ENST00000683605.1:n.319del
ENST00000684037.1:c.824del
ENST00000684061.1:n.958del
ENST00000684179.1:n.793del
ENST00000527805.6:c.824del
ENST00000675595.1:c.659del
ENST00000675843.1:c.824del
ENST00000278616.8:c.824del
ENST00000452508.6:c.824del
ENST00000527805.5:c.824del
NM_000051.3:c.824del
NM_001351834.1:c.824del
NM_001351834.2:c.824del
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Pathogenic

Met criteria codes 3
PM5_Supporting PVS1 PM3_Very Strong
Not Met criteria codes 3
PM2 BA1 BS1

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

Criteria Specification Approval History
Criteria Specifications for this VCEP
Evidence submitted by expert panel
Hereditary Breast, Ovarian and Pancreatic Cancer VCEP
The c.824del (p.Leu275Ter) variant in ATM is a frameshift 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 has been detected in at least 5 individuals with Ataxia-Telangiectasia (PMID: 26896183, 21792198, 9463314, 9887333). The c.824del (p.Leu275Ter) variant in ATM has a minor allele frequency in gnomAD v2.1.1 of 0.000018 in the non-Finnish European population (PM2_Supporting, BS1, and BA1 are not met). 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, PM5_Supporting, PM3_VeryStrong)
Met criteria codes
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
The c.824del (p.Leu275Ter) 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 (PVS1).
PM3_Very Strong
This variant has been detected in at least 5 individuals with Ataxia Telangiectasia. Of those individuals, 4 were compound heterozygous for the variant and another ATM variant and 2 of those were confirmed in trans by parental. 1 individual was homozygous for the variant (8 Points: PM3_VeryStrong; PMID 26896183, 21792198, 9463314, 9887333).
Not Met criteria codes
PM2
The c.824del (p.Leu275Ter) variant in ATM has a minor allele frequency in gnomAD v2.1.1 of 0.000018 in the non-Finnish European population (BA1, BS1, PM2_supporting not met).
BA1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BS1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
Curation History
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