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.5763-1050A>G

CA115927

3021 (ClinVar)

Gene: ATM
Condition: ATM-related cancer predisposition
Inheritance Mode: Autosomal dominant inheritance
UUID: b257c0e3-7ed5-432e-b2bc-7441d8c0b1dc
Approved on: 2024-11-26
Published on: 2025-01-13

HGVS expressions

NM_000051.4:c.5763-1050A>G
NM_000051.4(ATM):c.5763-1050A>G
NC_000011.10:g.108309110A>G
CM000673.2:g.108309110A>G
NC_000011.9:g.108179837A>G
CM000673.1:g.108179837A>G
NC_000011.8:g.107685047A>G
NG_009830.1:g.91279A>G
NG_054724.1:g.165723T>C
ENST00000452508.7:c.5763-1050A>G
ENST00000713593.1:c.*5234-1050A>G
ENST00000278616.9:c.5763-1050A>G
ENST00000525056.2:n.182-1050A>G
ENST00000682286.1:n.520-1050A>G
ENST00000682302.1:n.181-1050A>G
ENST00000683174.1:n.7247-1050A>G
ENST00000683524.1:n.987-1050A>G
ENST00000684152.1:n.1477-1050A>G
ENST00000527805.6:c.*827-1050A>G
ENST00000675595.1:c.*827-1050A>G
ENST00000675843.1:c.5763-1050A>G
ENST00000278616.8:c.5763-1050A>G
ENST00000452508.6:c.5763-1050A>G
ENST00000524792.5:n.1978-1050A>G
ENST00000525729.5:c.641-39T>C
ENST00000529588.5:c.187-1050A>G
ENST00000532765.1:n.79+1040A>G
ENST00000533690.5:n.1167-1050A>G
NM_000051.3:c.5763-1050A>G
NM_001330368.1:c.641-39T>C
NM_001351110.1:c.*39-39T>C
NM_001351834.1:c.5763-1050A>G
NM_001330368.2:c.641-39T>C
NM_001351110.2:c.*39-39T>C
NM_001351834.2:c.5763-1050A>G
More

Pathogenic

Met criteria codes 3
PVS1_Strong PP1_Strong PM3_Very Strong
Not Met criteria codes 2
PP3 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.5763-1050A>G variant in ATM is an intronic variant which results in an intronic A>G substitution before coding exon 38 activating a cryptic splice site leading to alternative splicing. The variant has been observed to cause an insertion of 137 nucleotides of intronic sequence at position 5762 and a premature stop codon at position 1930. Some normal splicing has been reported in patients with ATM c.5763-1050A>G, thus, the splice effect is incomplete (PMIDs 8755918, 10330348, 11382771, 15174027, Ambry internal data). This variant has been detected in many individuals with Ataxia-Telangiectasia, some of whom were described as having a mild presentation and/or later age of onset (PMIDs 8755918, 26896183). The variant has also been reported to segregate with Ataxia-Telangiectasia in 6 affected family members from 3 families (PMIDs 8755918, 15174027). The variant has a minor allele frequency in gnomAD v2.1.1 of 0.00003 (PM2_Supporting, BS1, and BA1 are not met). ATM c.5763-1050A>G has been reported as a founder variant in the British Isles (PMID 9463314). 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 VCEP. (PVS1_Strong (RNA), PM3_Very Strong, PP1_Strong)
Met criteria codes
PVS1_Strong
Near complete splicing effect, PVS1 strength reduced by one level to PVS1_RNA_strong. Approved by biocurator group based on publications below as well as Ambry internal data: observed r.5762_5763ins5762+985_5763-1055 p.P1922LFS*9 with a PSI generally around 20% (n >50 HET carriers). This splicing event is completely absent from Ambry non-carrier controls (n =373).
PP1_Strong
6 total affected segregations from 2 publications below. Per guidance from hearing loss VCEP (PMID: 30311386, table 4b), 6 affected segregations and 0 unaffected segregations results in a LOD score of 3.61 which is above the threshold of PP1_Strong (LOD 1.5).
PM3_Very Strong
Reported in several patients with AT diagnosis (11 points in total from publications below). 2 additional patients reported by Teraoka 1999 (PMID: 10330348) not counted as points already meets PM3_very strong.
Not Met criteria codes
PP3
No data available for splice prediction
PM2
Reported as a founder variant in the British Isles. Highest subpopulation frequency is 0.00008 which is above the threshold of 0.001%.
Curation History
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