Evidence Repository
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
  • 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.9145_9146del (p.Phe3049fs)

CA658797748

524412 (ClinVar)

Gene: ATM
Condition: ATM-related cancer predisposition
Inheritance Mode: Autosomal dominant inheritance
Link to MONDO
UUID: 68c62499-0db3-4c20-a327-cc40c84dc9a4
Approved on: 2025-06-11
Published on: 2025-07-10

HGVS expressions

NM_000051.4:c.9145_9146del
NM_000051.4(ATM):c.9145_9146del (p.Phe3049fs)
NC_000011.10:g.108365482_108365483del
CM000673.2:g.108365482_108365483del
NC_000011.9:g.108236209_108236210del
CM000673.1:g.108236209_108236210del
NC_000011.8:g.107741419_107741420del
NG_009830.1:g.147651_147652del
NG_054724.1:g.109352_109353del
ENST00000452508.7:c.9145_9146del
ENST00000713593.1:c.*8616_*8617del
ENST00000278616.9:c.9145_9146del
ENST00000638786.2:n.1843_1844del
ENST00000682286.1:n.3902_3903del
ENST00000682302.1:n.3563_3564del
ENST00000682569.1:n.2492_2493del
ENST00000683174.1:n.10629_10630del
ENST00000683524.1:n.4369_4370del
ENST00000684152.1:n.4561_4562del
ENST00000684180.1:n.1619_1620del
ENST00000684447.1:n.5638_5639del
ENST00000527805.6:c.*4209_*4210del
ENST00000675595.1:c.*4280_*4281del
ENST00000675843.1:c.9145_9146del
ENST00000278616.8:c.9145_9146del
ENST00000452508.6:c.9145_9146del
ENST00000524755.5:c.226+27727_226+27728del
ENST00000524792.5:n.5360_5361del
ENST00000525178.5:n.633_634del
ENST00000525729.5:c.640+20439_640+20440del
ENST00000526725.1:n.272-25117_272-25116del
ENST00000527181.1:n.484_485del
ENST00000527531.5:c.*2-9372_*2-9371del
ENST00000615746.4:c.*2-9372_*2-9371del
NM_000051.3:c.9145_9146del
NM_001330368.1:c.640+20439_640+20440del
NM_001351110.1:c.694+20439_694+20440del
NM_001351834.1:c.9145_9146del
NR_147053.2:n.1107-9372_1107-9371del
NM_001330368.2:c.640+20439_640+20440del
NM_001351110.2:c.694+20439_694+20440del
NM_001351834.2:c.9145_9146del
NR_147053.3:n.1105-9372_1105-9371del
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Uncertain Significance

Met criteria codes 3
PM2_Supporting PM3 PM4

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.9145_9146del variant in ATM is predicted to cause a change in the length of the protein (p.Phe3049Profs*13) due to a frameshift of 8 amino acids and an extension of an additional 4 amino acids. This variant has been detected in at least one individual with Ataxia-Telangiectasia (PMID: 10817650). This variant is absent from gnomAD v4.1.0. In summary, this variant meets the criteria to be classified as a variant of uncertain significance 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. (PM4, PM3, PM2_Supporting)
Met criteria codes
PM2_Supporting
This variant is absent from gnomAD v4.1.0 (PM2_Supporting).
PM3
This variant has been detected in 1 individual with Ataxia Telangiectasia. This individual also carried ATM c.264del but phase was not confirmed (2 points: PM3; PMID 10817650).
PM4
The c.9145_9146delTT variant is predicted to cause a change in the length of the protein (p.Phe3049Profs*13) due to a frameshift of 8 amino acids and an extension of an additional 4 amino acids (PM4).
Curation History
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