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
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Variant: NM_000051.4(ATM):c.8045C>G (p.Thr2682Ser)

CA382561906

644144 (ClinVar)

Gene: ATM (HGNC:472)
Condition: ATM-related cancer predisposition (MONDO:0700270)
Inheritance Mode: Autosomal dominant inheritance
UUID: cf42b25c-cac5-48e0-b3ca-83407767b8bb
Approved on: 2026-06-19
Published on: 2026-08-05

HGVS expressions

NM_000051.4:c.8045C>G
NM_000051.4(ATM):c.8045C>G (p.Thr2682Ser)
NC_000011.10:g.108335003C>G
CM000673.2:g.108335003C>G
NC_000011.9:g.108205730C>G
CM000673.1:g.108205730C>G
NC_000011.8:g.107710940C>G
NG_009830.1:g.117172C>G
NG_054724.1:g.139830G>C
ENST00000452508.7:c.8045C>G
ENST00000713593.1:c.*7516C>G
ENST00000278616.9:c.8045C>G
ENST00000525056.2:n.2464C>G
ENST00000638786.2:n.743C>G
ENST00000682286.1:n.2802C>G
ENST00000682302.1:n.2463C>G
ENST00000683174.1:n.9529C>G
ENST00000683524.1:n.3269C>G
ENST00000684152.1:n.3461C>G
ENST00000684180.1:n.519C>G
ENST00000684447.1:n.4538C>G
ENST00000527805.6:c.*3109C>G
ENST00000675595.1:c.*3180C>G
ENST00000675843.1:c.8045C>G
ENST00000278616.8:c.8045C>G
ENST00000452508.6:c.8045C>G
ENST00000524755.5:c.299+217G>C
ENST00000524792.5:n.4260C>G
ENST00000525056.1:n.242C>G
ENST00000525729.5:c.641-25932G>C
ENST00000527531.5:c.*1269+217G>C
ENST00000533979.5:n.257C>G
ENST00000615746.4:c.*1269+217G>C
NM_000051.3:c.8045C>G
NM_001330368.1:c.641-25932G>C
NM_001351110.1:c.*38+217G>C
NM_001351834.1:c.8045C>G
NR_147053.2:n.2374+217G>C
NM_001330368.2:c.641-25932G>C
NM_001351110.2:c.*38+217G>C
NM_001351834.2:c.8045C>G
NR_147053.3:n.2372+217G>C
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Pathogenic

Met criteria codes 3
PM3_Supporting PVS1 PM2_Supporting
Not Met criteria codes 1
PP3

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 1.4.0

Criteria Specification Approval History
Criteria Specifications for this VCEP
Evidence submitted by expert panel
Hereditary Breast, Ovarian and Pancreatic Cancer VCEP
The c.8045C>G variant in ATM is a missense variant predicted to cause substitution of threonine by serine at amino acid 2682 (p.Thr2682Ser). This variant has been detected in individual(s) with Ataxia-Telangiectasia (PMID: 12815592). The highest population minor allele frequency in gnomAD v4.1.0 is 0.0.00002229 (1/44868alleles) in East Asian 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. The computational splicing predictor SpliceAI gives a score of 0.97 for donor gain, predicting that the variant disrupts the donor splice site of ATM. RNA analysis demonstrated that this variant leads to partial skipping of exon 54, resulting in an in-frame deletion (removes amino acids 2681-2717) that is predicted to escape nonsense mediated decay but adversely impact the FATKIN domain (Ambry internal data). 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. (PM3_Supporting, PM2_Supporting, PVS1[RNA]).
Met criteria codes
PM3_Supporting
PMID: 12815592 This variant has been observed in an individual(In the list of variants detected from Iberian population(18 Hispanic-American families) with ataxia telangiectasia (A-T Patients) in Trans (Phased confirmed) with another ATM variant c.8150A>C (called LP by VCEP). *Of note, a clerical error previously listed that this variant co-occurred with c.8150T>G.
PVS1
This variant leads to partial skipping of exon 54 (Ambry internal data), PVS1 (RNA)
PM2_Supporting
The highest population minor allele frequency in gnomAD v4.1.0 is 0.0.00002229 (1/44868alleles) in East Asian 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.
Not Met criteria codes
PP3
Applying PVS1[RNA] The computational splicing predictor SpliceAI gives a score of 0.97 for donor gain, predicting that the variant disrupts the donor splice site of ATM.
Curation History
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