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NM_000179.2(MSH6):c.3557-4dup

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Interpretation:
Benign​

Review status:
reviewed by expert panel
Submissions:
7 (Most recent: Aug 19, 2021)
Last evaluated:
Sep 5, 2013
Accession:
VCV000089418.5
Variation ID:
89418
Description:
1bp duplication
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NM_000179.2(MSH6):c.3557-4dup

Allele ID
94892
Variant type
Duplication
Variant length
1 bp
Cytogenetic location
2p16.3
Genomic location
2: 47805601-47805602 (GRCh38) GRCh38 UCSC
2: 48032740-48032741 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000002.11:g.48032753dup
NC_000002.12:g.47805614dup
NM_001281493.1:c.2651-4dup
... more HGVS
Protein change
-
Other names
-
Canonical SPDI
NC_000002.12:47805601:TTTTTTTTTTTTT:TTTTTTTTTTTTTT
Functional consequence
-
Global minor allele frequency (GMAF)
-

Allele frequency
-
Links
ClinGen: CA013400
dbSNP: rs267608102
Varsome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Benign 1 reviewed by expert panel Sep 5, 2013 RCV000074886.2
Benign/Likely benign 2 criteria provided, multiple submitters, no conflicts Dec 1, 2014 RCV000162507.4
Benign 3 criteria provided, single submitter Feb 7, 2019 RCV000584641.3
Benign 1 no assertion criteria provided - RCV000613784.1
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
MSH6 Sufficient evidence for dosage pathogenicity No evidence available GRCh38
GRCh37
5633 5667

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
no known pathogenicity
(Sep 05, 2013)
reviewed by expert panel
Method: research
Lynch Syndrome
Allele origin: germline
International Society for Gastrointestinal Hereditary Tumours (InSiGHT)
Accession: SCV000108099.2
Submitted: (Dec 18, 2013)
Comment:
Classified with v1.9 guidelines: https://docs.google.com/file/d/0B3JL6rP6JzhoN2EydHRVMEI1UGs
Evidence details
Comments (2):
MAF >1%
Converted during submission to Benign.
Benign
(Dec 01, 2014)
criteria provided, single submitter
Method: clinical testing
Hereditary cancer-predisposing syndrome
Allele origin: germline
Color Health, Inc
Accession: SCV000690369.2
Submitted: (May 19, 2020)
Evidence details
Benign
(Feb 07, 2019)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
Women's Health and Genetics/Laboratory Corporation of America, LabCorp
Accession: SCV001360589.1
Submitted: (Mar 06, 2020)
Evidence details
Publications
PubMed (3)
Comment:
Variant summary: MSH6 c.3557-4dupT alters a non-conserved nucleotide located close to a canonical splice site and therefore could affect mRNA splicing, leading to a significantly … (more)
Likely benign
(Nov 06, 2012)
criteria provided, single submitter
Method: clinical testing
Hereditary cancer-predisposing syndrome
Allele origin: germline
Ambry Genetics
Accession: SCV000212898.5
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)
Benign
(-)
no assertion criteria provided
Method: clinical testing
not specified
Allele origin: unknown
Mayo Clinic Laboratories, Mayo Clinic
Accession: SCV000691940.1
Submitted: (Oct 31, 2017)
Evidence details
Benign
(-)
no assertion criteria provided
Method: clinical testing
Hereditary nonpolyposis colorectal cancer type 5
Allele origin: germline
Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen
Study: VKGL Data-share Consensus
Accession: SCV000734221.1
Submitted: (Apr 04, 2018)
Evidence details
Benign
(-)
no assertion criteria provided
Method: clinical testing
not specified
Allele origin: germline
Laboratory of Diagnostic Genome Analysis, Leiden University Medical Center (LUMC)
Study: VKGL Data-share Consensus
Accession: SCV001800145.1
Submitted: (Aug 19, 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
Association of rare MSH6 variants with familial breast cancer. Wasielewski M Breast cancer research and treatment 2010 PMID: 19924528
No MSH6 germline mutations in breast cancer families with colorectal and/or endometrial cancer. Vahteristo P Journal of medical genetics 2005 PMID: 15805151
Do MSH6 mutations contribute to double primary cancers of the colorectum and endometrium? Charames GS Human genetics 2000 PMID: 11153917
http://www.insight-database.org/classifications/index.html?gene=MSH6&variant=c.3557-4dup - - - -

Text-mined citations for rs267608102...

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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 Aug 25, 2021