NM_000051.4(ATM):c.2921+1G>C AND not provided

Clinical significance:Pathogenic (Last evaluated: Nov 21, 2016)

Review status:1 star out of maximum of 4 stars

criteria provided, single submitter

Based on:
1 submission [Details]
Record status:
current
Accession:
RCV000236109.2

Allele description [Variation Report for NM_000051.4(ATM):c.2921+1G>C]

NM_000051.4(ATM):c.2921+1G>C

Gene:
ATM:ATM serine/threonine kinase [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
11q22.3
Genomic location:
Preferred name:
NM_000051.4(ATM):c.2921+1G>C
HGVS:
  • NC_000011.10:g.108271147G>C
  • NG_009830.1:g.53316G>C
  • NM_000051.4:c.2921+1G>CMANE SELECT
  • NM_001351834.2:c.2921+1G>C
  • LRG_135t1:c.2921+1G>C
  • LRG_135:g.53316G>C
  • NC_000011.9:g.108141874G>C
  • NM_000051.3:c.2921+1G>C
Links:
dbSNP: rs587781558
NCBI 1000 Genomes Browser:
rs587781558
Molecular consequence:
  • NM_000051.4:c.2921+1G>C - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001351834.2:c.2921+1G>C - splice donor variant - [Sequence Ontology: SO:0001575]

Condition(s)

Identifiers:
MedGen: CN517202

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000293826GeneDxcriteria provided, single submitter
Pathogenic
(Nov 21, 2016)
germlineclinical testing

Citation Link

Summary from all submissions

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

Details of each submission

From GeneDx, SCV000293826.10

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

Description

This variant is denoted ATM c.2921+1G>C or IVS19+1G>C and consists of a G>C nucleotide substitution at the +1 position of intron 19 of the ATM gene. This variant destroys a canonical splice donor site and is predicted to cause abnormal gene splicing, leading to either an abnormal message that is subject to nonsense-mediated mRNA decay or to an abnormal protein product. Although c.2921+1G>C has not, to our knowledge, been published in the literature, another nucleotide change at this position, c.2921+1G>A, has been reported in multiple cases of classical Ataxia-telangiectasia and resulted in complete loss of the adjacent exon (Gilad 1996, García-Pérez 2001, Mitui 2003). Based on the current evidence, we consider ATM c.2921+1G>C to be pathogenic.

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

Last Updated: Nov 27, 2021

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