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NM_000051.4(ATM):c.5763-1056G>A AND ATM-related disorder

Germline classification:
Likely pathogenic (1 submission)
Last evaluated:
May 16, 2024
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Somatic classification
of clinical impact:
None
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Somatic classification
of oncogenicity:
None
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Record status:
current
Accession:
RCV004548253.4

Allele description [Variation Report for NM_000051.4(ATM):c.5763-1056G>A]

NM_000051.4(ATM):c.5763-1056G>A

Genes:
ATM:ATM serine/threonine kinase [Gene - OMIM - HGNC]
C11orf65:chromosome 11 open reading frame 65 [Gene - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
11q22.3
Genomic location:
Preferred name:
NM_000051.4(ATM):c.5763-1056G>A
HGVS:
  • NC_000011.10:g.108309104G>A
  • NG_009830.1:g.91273G>A
  • NG_054724.1:g.165729C>T
  • NM_000051.4:c.5763-1056G>AMANE SELECT
  • NM_001330368.2:c.641-33C>T
  • NM_001351110.2:c.*39-33C>T
  • NM_001351834.2:c.5763-1056G>A
  • LRG_135t1:c.5763-1056G>A
  • LRG_135:g.91273G>A
  • NC_000011.9:g.108179831G>A
  • NM_000051.3:c.5763-1056G>A
Links:
dbSNP: rs1325461375
NCBI 1000 Genomes Browser:
rs1325461375
Molecular consequence:
  • NM_000051.4:c.5763-1056G>A - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001330368.2:c.641-33C>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001351110.2:c.*39-33C>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001351834.2:c.5763-1056G>A - intron variant - [Sequence Ontology: SO:0001627]

Condition(s)

Name:
ATM-related disorder
Synonyms:
ATM-related disorders; ATM-related condition
Identifiers:

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV004780311PreventionGenetics, part of Exact Sciences
no assertion criteria provided
Likely pathogenic
(May 16, 2024) 		germlineclinical testing

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing

Details of each submission

From PreventionGenetics, part of Exact Sciences, SCV004780311.3

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided

Description

The ATM c.5763-1056G>A variant is predicted to interfere with splicing. This variant has been reported in an individual with breast cancer, and RNAseq studies suggest this variant impacts mRNA splicing (Dragoš et al. 2022. PubMed ID: 35806449). This variant is reported in 0.0021% of alleles in individuals of European (non-Finnish) descent in gnomAD. It has conflicting classifications listed in ClinVar, ranging from likely pathogenic to uncertain significance (https://www.ncbi.nlm.nih.gov/clinvar/variation/1696413/). This variant is interpreted as likely pathogenic.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Nov 3, 2024