NM_000251.3(MSH2):c.792+5A>G AND not provided

Clinical significance:Uncertain significance (Last evaluated: Dec 16, 2016)

Review status:1 star out of maximum of 4 stars

criteria provided, single submitter

Based on:
1 submission [Details]
Record status:
current
Accession:
RCV000589455.1

Allele description [Variation Report for NM_000251.3(MSH2):c.792+5A>G]

NM_000251.3(MSH2):c.792+5A>G

Gene:
MSH2:mutS homolog 2 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
2p21
Genomic location:
Preferred name:
NM_000251.3(MSH2):c.792+5A>G
HGVS:
  • NC_000002.12:g.47412565A>G
  • NG_007110.2:g.14442A>G
  • NM_000251.2:c.792+5A>G
  • NM_000251.3:c.792+5A>GMANE SELECT
  • NM_001258281.1:c.594+5A>G
  • LRG_218t1:c.792+5A>G
  • LRG_218:g.14442A>G
  • NC_000002.11:g.47639704A>G
  • NM_000251.1:c.792+5A>G
Links:
dbSNP: rs267607935
NCBI 1000 Genomes Browser:
rs267607935
Molecular consequence:
  • NM_000251.2:c.792+5A>G - intron variant - [Sequence Ontology: SO:0001627]
  • NM_000251.3:c.792+5A>G - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001258281.1:c.594+5A>G - intron variant - [Sequence Ontology: SO:0001627]

Condition(s)

Identifiers:
MedGen: CN517202

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000696283Women's Health and Genetics/Laboratory Corporation of America, LabCorpcriteria provided, single submitter
Uncertain significance
(Dec 16, 2016)
germlineclinical testing

PubMed (1)
[See all records that cite this PMID]

LabCorp Variant Classification Summary - May 2015.docx

Citation Link

Summary from all submissions

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

Citations

PubMed

Multiple rare variants in different genes account for multifactorial inherited susceptibility to colorectal adenomas.

Fearnhead NS, Wilding JL, Winney B, Tonks S, Bartlett S, Bicknell DC, Tomlinson IP, Mortensen NJ, Bodmer WF.

Proc Natl Acad Sci U S A. 2004 Nov 9;101(45):15992-7. Epub 2004 Nov 1.

PubMed [citation]
PMID:
15520370
PMCID:
PMC528777

Details of each submission

From Women's Health and Genetics/Laboratory Corporation of America, LabCorp, SCV000696283.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)

Description

Variant summary: The MSH2 c.792+5A>G variant involves the alteration of a non-conserved intronic nucleotide. One in silico tool predicts a benign outcome for this variant. 5/5 splice prediction tools predict the variant to result in the strengthening of a cannonical splice donor site. However, these predictions have yet to be confirmed by functional studies. This variant was found in 3/119958 control chromosomes at a frequency of 0.000025, which does not exceed the estimated maximal expected allele frequency of a pathogenic MSH2 variant (0.0005683). The variant was reported in an affected individual in the literature, without strong evidence for causality. In addition, multiple clinical diagnostic laboratories/reputable databases classified this variant as uncertain significance. Taken together, this variant is classified as VUS.

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

Last Updated: Oct 30, 2021

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