NM_000251.3(MSH2):c.115C>A (p.Arg39=) AND not specified

Clinical significance:Uncertain significance (Last evaluated: Dec 15, 2019)

Review status:1 star out of maximum of 4 stars

criteria provided, single submitter

Based on:
1 submission [Details]
Record status:

Allele description [Variation Report for NM_000251.3(MSH2):c.115C>A (p.Arg39=)]

NM_000251.3(MSH2):c.115C>A (p.Arg39=)

MSH2:mutS homolog 2 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
Genomic location:
Preferred name:
NM_000251.3(MSH2):c.115C>A (p.Arg39=)
  • NC_000002.12:g.47403306C>A
  • NG_007110.2:g.5183C>A
  • NM_000251.3:c.115C>AMANE SELECT
  • NM_001258281.1:c.-30-54C>A
  • NP_000242.1:p.Arg39=
  • NP_000242.1:p.Arg39=
  • LRG_218t1:c.115C>A
  • LRG_218:g.5183C>A
  • LRG_218p1:p.Arg39=
  • NC_000002.11:g.47630445C>A
  • NM_000251.1:c.115C>A
  • NM_000251.2:c.115C>A
  • p.R39R
dbSNP: rs786202334
NCBI 1000 Genomes Browser:
Molecular consequence:
  • NM_001258281.1:c.-30-54C>A - intron variant - [Sequence Ontology: SO:0001627]
  • NM_000251.3:c.115C>A - synonymous variant - [Sequence Ontology: SO:0001819]


MedGen: CN169374

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
SCV001363059Women's Health and Genetics/Laboratory Corporation of America, LabCorpcriteria provided, single submitter
Uncertain significance
(Dec 15, 2019)
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, SCV001363059.1

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


Variant summary: MSH2 c.115C>A alters a conserved nucleotide resulting in a synonymous change. Several computational tools predict a significant impact on normal splicing: Five predict the variant creates a cryptic exonic 3' acceptor site. However, these predictions have yet to be confirmed by functional studies. The variant allele was found at a frequency of 2.2e-05 in 226718 control chromosomes. The available data on variant occurrences in the general population are insufficient to allow any conclusion about variant significance. To our knowledge, no occurrence of c.115C>A in individuals affected with Lynch Syndrome and no experimental evidence demonstrating its impact on protein function have been reported. Four clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014 without evidence for independent evaluation (likely benign, n=3; VUS, n=1). Based on the evidence outlined above, the variant was classified as VUS-possibly benign.

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

Last Updated: Dec 4, 2021

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