NM_000051.3(ATM):c.6338C>G (p.Thr2113Ser) AND not specified

Clinical significance:Uncertain significance (Last evaluated: Feb 24, 2020)

Review status:1 star out of maximum of 4 stars

criteria provided, single submitter

Based on:
1 submission [Details]
Record status:
current
Accession:
RCV001174836.1

Allele description [Variation Report for NM_000051.3(ATM):c.6338C>G (p.Thr2113Ser)]

NM_000051.3(ATM):c.6338C>G (p.Thr2113Ser)

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.6338C>G (p.Thr2113Ser)
HGVS:
  • NC_000011.10:g.108317512C>G
  • NG_009830.1:g.99681C>G
  • NG_054724.1:g.157321G>C
  • NM_000051.3:c.6338C>G
  • NM_001330368.2:c.641-8441G>C
  • NM_001351110.2:c.39-8441G>C
  • NM_001351834.2:c.6338C>G
  • NP_000042.3:p.Thr2113Ser
  • NP_001338763.1:p.Thr2113Ser
  • LRG_135t1:c.6338C>G
  • LRG_135:g.99681C>G
  • LRG_135p1:p.Thr2113Ser
  • NC_000011.9:g.108188239C>G
Protein change:
T2113S
Links:
dbSNP: rs573290117
NCBI 1000 Genomes Browser:
rs573290117
Molecular consequence:
  • NM_001330368.2:c.641-8441G>C - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001351110.2:c.39-8441G>C - intron variant - [Sequence Ontology: SO:0001627]
  • NM_000051.3:c.6338C>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001351834.2:c.6338C>G - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Synonyms:
AllHighlyPenetrant
Identifiers:
MedGen: CN169374

Recent activity

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

See more...

Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV001338210Women's Health and Genetics/Laboratory Corporation of America, LabCorpcriteria provided, single submitter
Uncertain significance
(Feb 24, 2020)
germlineclinical testing

Citation Link

Summary from all submissions

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

Details of each submission

From Women's Health and Genetics/Laboratory Corporation of America, LabCorp, SCV001338210.1

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

Description

Variant summary: ATM c.6338C>G (p.Thr2113Ser) results in a conservative amino acid change located in the PIK-related kinase, FAT domain (IPR003151) of the encoded protein sequence. Five of five in-silico tools predict a benign effect of the variant on protein function. The variant allele was found at a frequency of 4.8e-05 in 249878 control chromosomes (gnomAD). This frequency is not higher than expected for a pathogenic variant in ATM causing Breast Cancer (4.8e-05 vs 0.001), allowing no conclusion about variant significance. To our knowledge, no occurrence of c.6338C>G in individuals affected with Breast Cancer and no experimental evidence demonstrating its impact on protein function have been reported. Three ClinVar submitters (evaluation after 2014) cite the variant as uncertain significance (2x) and likely benign (1x). Based on the evidence outlined above, the variant was classified as uncertain significance.

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

Last Updated: Aug 27, 2021

Support Center