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NM_000251.2(MSH2):c.2211-10T>A

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Interpretation:
Conflicting interpretations of pathogenicity​

Likely pathogenic(1);Uncertain significance(3)

Review status:
criteria provided, conflicting interpretations
Submissions:
4 (Most recent: Jan 7, 2021)
Last evaluated:
Oct 20, 2020
Accession:
VCV000090927.9
Variation ID:
90927
Description:
single nucleotide variant
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NM_000251.2(MSH2):c.2211-10T>A

Allele ID
96402
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
2p21
Genomic location
2: 47478262 (GRCh38) GRCh38 UCSC
2: 47705401 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000002.11:g.47705401T>A
NC_000002.12:g.47478262T>A
NM_001258281.1:c.2013-10T>A
... more HGVS
Protein change
-
Other names
-
Canonical SPDI
NC_000002.12:47478261:T:A
Functional consequence
-
Global minor allele frequency (GMAF)
-

Allele frequency
The Genome Aggregation Database (gnomAD), exomes 0.00000
Links
ClinGen: CA020271
dbSNP: rs267608006
Varsome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Uncertain significance 1 criteria provided, single submitter Jul 13, 2018 RCV000478566.2
Uncertain significance 1 criteria provided, single submitter Oct 20, 2020 RCV000791387.3
Conflicting interpretations of pathogenicity 2 criteria provided, conflicting interpretations Aug 21, 2020 RCV000491555.6
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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
4498 4583

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Uncertain significance
(Jul 13, 2018)
criteria provided, single submitter
Method: clinical testing
Not Provided
Allele origin: germline
GeneDx
Accession: SCV000569683.5
Submitted: (Jan 29, 2019)
Evidence details
Comment:
This variant is denoted MSH2 c.2211-10T>A or IVS13-10T>A and consists of a T>A nucleotide substitution at the -10 position of intron 13 of the MSH2 … (more)
Likely pathogenic
(Aug 21, 2020)
criteria provided, single submitter
Method: clinical testing
Hereditary cancer-predisposing syndrome
Allele origin: germline
Ambry Genetics
Accession: SCV000580509.4
Submitted: (Nov 30, 2020)
Evidence details
Comment:
​The c.2211-10T>A intronic variant results from a T to A substitution 10 nucleotides before coding exon 14 in the MSH2 gene. This variant has been … (more)
Uncertain significance
(Mar 03, 2020)
criteria provided, single submitter
Method: clinical testing
Hereditary cancer-predisposing syndrome
Allele origin: germline
Color Health, Inc
Accession: SCV000903947.2
Submitted: (May 19, 2020)
Comment:
This variant causes a T to A nucleotide substitution at the -10 position of intron 13 of the MSH2 gene. Splice site prediction tools predict … (more)
Evidence details
Uncertain significance
(Oct 20, 2020)
criteria provided, single submitter
Method: clinical testing
Hereditary nonpolyposis colorectal neoplasms
Allele origin: germline
Invitae
Accession: SCV000260343.5
Submitted: (Jan 07, 2021)
Evidence details
Publications
PubMed (1)
Comment:
This sequence change falls in intron 13 of the MSH2 gene. It does not directly change the encoded amino acid sequence of the MSH2 protein. … (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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Title Author Journal Year Link
MSH6 mutation in Muir-Torre syndrome: could this be a rare finding? Mangold E The British journal of dermatology 2007 PMID: 17199584

Text-mined citations for rs267608006...

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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 Apr 12, 2021