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NM_000251.2(MSH2):c.367-19A>T

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Interpretation:
Benign/Likely benign​

Review status:
criteria provided, multiple submitters, no conflicts
Submissions:
4 (Most recent: Sep 9, 2020)
Last evaluated:
Aug 10, 2020
Accession:
VCV000182607.3
Variation ID:
182607
Description:
single nucleotide variant
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NM_000251.2(MSH2):c.367-19A>T

Allele ID
179987
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
2p21
Genomic location
2: 47410075 (GRCh38) GRCh38 UCSC
2: 47637214 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000002.11:g.47637214A>T
NC_000002.12:g.47410075A>T
NM_001258281.1:c.169-19A>T
... more HGVS
Protein change
-
Other names
-
Canonical SPDI
NC_000002.12:47410074:A:T
Functional consequence
-
Global minor allele frequency (GMAF)
-

Allele frequency
Trans-Omics for Precision Medicine (TOPMed) 0.00011
The Genome Aggregation Database (gnomAD), exomes 0.00005
Exome Aggregation Consortium (ExAC) 0.00005
The Genome Aggregation Database (gnomAD) 0.00006
Links
ClinGen: CA021067
dbSNP: rs730881783
Varsome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Benign/Likely benign 2 criteria provided, multiple submitters, no conflicts Aug 10, 2020 RCV000160650.4
Likely benign 1 criteria provided, single submitter Oct 25, 2016 RCV000412430.1
Likely benign 1 criteria provided, single submitter Apr 17, 2016 RCV000580191.1
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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
4480 4565

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Likely benign
(Oct 25, 2016)
criteria provided, single submitter
Method: clinical testing
Lynch syndrome I
Allele origin: unknown
Counsyl
Accession: SCV000489597.1
Submitted: (Nov 23, 2016)
Evidence details
Likely benign
(Apr 17, 2016)
criteria provided, single submitter
Method: clinical testing
Hereditary cancer-predisposing syndrome
Allele origin: germline
Color Health, Inc
Accession: SCV000685085.1
Submitted: (Oct 26, 2017)
Evidence details
Likely benign
(Aug 10, 2020)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
Women's Health and Genetics/Laboratory Corporation of America, LabCorp
Accession: SCV000917722.2
Submitted: (Sep 09, 2020)
Evidence details
Comment:
Variant summary: MSH2 c.367-19A>T alters a non-conserved nucleotide located close to a canonical splice site and therefore could affect mRNA splicing, leading to a significantly … (more)
Benign
(Jan 29, 2014)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
GeneDx
Accession: SCV000211252.10
Submitted: (Mar 26, 2018)
Evidence details
Comment:
This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at … (more)

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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There are no citations in ClinVar for this variation. If you know of citations for this variation, please consider submitting that information to ClinVar.

Text-mined citations for rs730881783...

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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 Jun 14, 2021