NM_000051.3(ATM):c.7988T>C (p.Val2663Ala) AND not provided

Clinical significance:Uncertain significance (Last evaluated: Oct 17, 2018)

Review status:1 star out of maximum of 4 stars

criteria provided, single submitter

Based on:
1 submission [Details]
Record status:
current
Accession:
RCV000656763.2

Allele description [Variation Report for NM_000051.3(ATM):c.7988T>C (p.Val2663Ala)]

NM_000051.3(ATM):c.7988T>C (p.Val2663Ala)

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_000051.3(ATM):c.7988T>C (p.Val2663Ala)
Other names:
p.V2663A:GTT>GCT
HGVS:
  • NC_000011.10:g.108333946T>C
  • NG_009830.1:g.116115T>C
  • NG_054724.1:g.140887A>G
  • NM_000051.3:c.7988T>C
  • NM_001330368.2:c.641-24875A>G
  • NM_001351110.2:c.38+1274A>G
  • NM_001351834.2:c.7988T>C
  • NP_000042.3:p.Val2663Ala
  • NP_001338763.1:p.Val2663Ala
  • LRG_135t1:c.7988T>C
  • LRG_135:g.116115T>C
  • LRG_135p1:p.Val2663Ala
  • NC_000011.9:g.108204673T>C
Protein change:
V2663A
Links:
dbSNP: rs377648506
NCBI 1000 Genomes Browser:
rs377648506
Molecular consequence:
  • NM_001330368.2:c.641-24875A>G - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001351110.2:c.38+1274A>G - intron variant - [Sequence Ontology: SO:0001627]
  • NM_000051.3:c.7988T>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001351834.2:c.7988T>C - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Identifiers:
MedGen: CN517202

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000209650GeneDxcriteria provided, single submitter
Uncertain significance
(Oct 17, 2018)
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, SCV000209650.14

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

Description

This variant is denoted ATM c.7988T>C at the cDNA level, p.Val2663Ala (V2663A) at the protein level, and results in the change of a Valine to an Alanine (GTT>GCT). This variant has been observed in at least one individual with breast cancer and another with thyroid cancer (Tung 2016, Yehia 2018). Additionally, ATM Val2663Ala was identified in 1/46 healthy African-European individuals undergoing whole exome sequencing (Bodian 2014). Of note, the participants in this study were younger than 50 years old thus the unaffected status of this individual may not be significant. ATM Val2663Ala was observed at an allele frequency of 0.05% (12/24028) in individuals of African ancestry in large population cohorts (Lek 2016). ATM Val2663Ala is not located in a known functional domain. In-silico analysis, which includes protein predictors and evolutionary conservation, supports that this variant does not alter protein structure/function. Based on currently available evidence, it is unclear whether ATM Val2663Ala is a pathogenic or benign variant. We consider it to be a variant of uncertain significance.

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

Last Updated: Jun 14, 2021

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