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

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Interpretation:
Conflicting interpretations of pathogenicity​

Likely benign(4);Uncertain significance(2)

Review status:
criteria provided, conflicting interpretations
Submissions:
6 (Most recent: Sep 25, 2021)
Last evaluated:
Oct 19, 2020
Accession:
VCV000185640.8
Variation ID:
185640
Description:
single nucleotide variant
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NM_000251.3(MSH2):c.115C>A (p.Arg39=)

Allele ID
181895
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
2p21
Genomic location
2: 47403306 (GRCh38) GRCh38 UCSC
2: 47630445 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
LRG_218:g.5183C>A
LRG_218t1:c.115C>A LRG_218p1:p.Arg39=
NC_000002.12:g.47403306C>A
... more HGVS
Protein change
-
Other names
-
Canonical SPDI
NC_000002.12:47403305:C:A
Functional consequence
-
Global minor allele frequency (GMAF)
-

Allele frequency
Trans-Omics for Precision Medicine (TOPMed) 0.00002
The Genome Aggregation Database (gnomAD) 0.00001
Trans-Omics for Precision Medicine (TOPMed) 0.00001
The Genome Aggregation Database (gnomAD), exomes 0.00002
The Genome Aggregation Database (gnomAD) 0.00003
Links
ClinGen: CA017385
dbSNP: rs786202334
VarSome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Likely benign 2 criteria provided, multiple submitters, no conflicts Apr 24, 2017 RCV000165094.2
Uncertain significance 1 criteria provided, single submitter Oct 19, 2020 RCV000233469.7
Uncertain significance 1 criteria provided, single submitter Dec 15, 2019 RCV000427878.4
Likely benign 1 criteria provided, single submitter Mar 26, 2018 RCV000663112.1
Likely benign 1 criteria provided, single submitter Jun 10, 2020 RCV001704201.1
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
MSH2 Sufficient evidence for dosage pathogenicity No evidence available GRCh38
GRCh37
4521 4606

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Likely benign
(Jul 25, 2014)
criteria provided, single submitter
Method: clinical testing
Hereditary cancer-predisposing syndrome
Allele origin: germline
Ambry Genetics
Accession: SCV000215802.5
Submitted: (Nov 30, 2020)
Evidence details
Comment:
This alteration is classified as likely benign based on a combination of the following: population frequency, intact protein function, lack of segregation with disease, co-occurrence, … (more)
Uncertain significance
(Oct 19, 2020)
criteria provided, single submitter
Method: clinical testing
Hereditary nonpolyposis colorectal neoplasms
Allele origin: germline
Invitae
Accession: SCV000284093.7
Submitted: (Jan 07, 2021)
Evidence details
Publications
PubMed (1)
Comment:
This sequence change affects codon 39 of the MSH2 mRNA. It is a 'silent' change, meaning that it does not change the encoded amino acid … (more)
Likely benign
(Apr 24, 2017)
criteria provided, single submitter
Method: clinical testing
Hereditary cancer-predisposing syndrome
Allele origin: germline
Color Health, Inc
Accession: SCV000689959.1
Submitted: (Dec 21, 2017)
Evidence details
Likely benign
(Mar 26, 2018)
criteria provided, single submitter
Method: clinical testing
Lynch syndrome I
Allele origin: unknown
Counsyl
Accession: SCV000786240.2
Submitted: (Jun 20, 2018)
Evidence details
Uncertain significance
(Dec 15, 2019)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
Women's Health and Genetics/Laboratory Corporation of America, LabCorp
Accession: SCV001363059.1
Submitted: (Mar 06, 2020)
Evidence details
Comment:
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 … (more)
Likely benign
(Jun 10, 2020)
criteria provided, single submitter
Method: clinical testing
Not Provided
Allele origin: germline
GeneDx
Accession: SCV000530573.4
Submitted: (Sep 25, 2021)
Evidence details

Functional evidence

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There is no functional evidence in ClinVar for this variation. If you have generated functional data for this variation, please consider submitting that data to ClinVar.

Citations for this variant

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Title Author Journal Year Link
Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria. Nykamp K Genetics in medicine : official journal of the American College of Medical Genetics 2017 PMID: 28492532

Text-mined citations for rs786202334...

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These citations are identified by LitVar using the rs number, so they may include citations for more than one variant at this location. Please review the LitVar results carefully for your variant of interest.

Record last updated Nov 27, 2021