NM_000051.4(ATM):c.2839-4T>C AND not provided

Clinical significance:Likely benign (Last evaluated: Jul 31, 2020)

Review status:1 star out of maximum of 4 stars

criteria provided, single submitter

Based on:
2 submissions [Details]
Record status:

Allele description [Variation Report for NM_000051.4(ATM):c.2839-4T>C]


ATM:ATM serine/threonine kinase [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
Genomic location:
Preferred name:
  • NC_000011.10:g.108271060T>C
  • NG_009830.1:g.53229T>C
  • NM_000051.4:c.2839-4T>CMANE SELECT
  • NM_001351834.2:c.2839-4T>C
  • LRG_135t1:c.2839-4T>C
  • LRG_135:g.53229T>C
  • NC_000011.9:g.108141787T>C
  • NM_000051.3:c.2839-4T>C
dbSNP: rs1057522619
NCBI 1000 Genomes Browser:
Molecular consequence:
  • NM_000051.4:c.2839-4T>C - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001351834.2:c.2839-4T>C - intron variant - [Sequence Ontology: SO:0001627]


MedGen: CN517202

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
SCV000528643GeneDxcriteria provided, single submitter
Likely benign
(Jul 31, 2020)
germlineclinical testing

Citation Link,

SCV001553133Department of Pathology and Laboratory Medicine,Sinai Health System - The Canadian Open Genetics Repository (COGR)

See additional submitters

no assertion criteria providedUncertain significanceunknownclinical testing

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedunknownyes1not providednot providednot providednot providedclinical testing
not providedgermlineyesnot providednot providednot providednot providednot providedclinical testing

Details of each submission

From GeneDx, SCV000528643.4

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot providednot providednot providednot providednot provided

From Department of Pathology and Laboratory Medicine,Sinai Health System - The Canadian Open Genetics Repository (COGR), SCV001553133.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided1not providednot providedclinical testingnot provided


The ATM c.2839-4T>C variant was not identified in the literature nor was it identified in the following databases: dbSNP, COGR, Cosmic, LOVD 3.0, and ATM-LOVD. The variant was identified in ClinVar (classified as likely benign by GeneDx and Invitae and classified as uncertain significance by Ambry Genetics). The variant was also not identified in the following control databases: the 1000 Genomes Project, the NHLBI GO Exome Sequencing Project, the Exome Aggregation Consortium (August 8th 2016), or the Genome Aggregation Database (Feb 27, 2017). The c.2839-4T>C variant is located in the 3' splice region but does not affect the invariant -1 or -2 positions. Positions -3 and -5 to -12 are also part of the splicing consensus sequence and variants involving these positions sometimes affect splicing; however, this variant is not located at any of these positions. Further, only 1 of 4 in silico or computational prediction software programs (SpliceSiteFinder, MaxEntScan, NNSPLICE, GeneSplicer) predicts a greater than 10% difference in splicing. In summary, based on the above information, the clinical significance of this variant cannot be determined with certainty at this time. This variant is classified as a variant of uncertain significance.

OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1unknownyesnot providednot providednot provided1not providednot providednot provided

Last Updated: Nov 27, 2021

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