Skip to main page content
Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation

ClinVar Genomic variation as it relates to human health

Advanced search

NM_000179.2(MSH6):c.-159C>T

Help
Interpretation:
Benign​

Review status:
reviewed by expert panel
Submissions:
3 (Most recent: Sep 9, 2021)
Last evaluated:
Sep 5, 2013
Accession:
VCV000089158.4
Variation ID:
89158
Description:
single nucleotide variant
Help

NM_000179.2(MSH6):c.-159C>T

Allele ID
94632
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
2p16.3
Genomic location
2: 47783075 (GRCh38) GRCh38 UCSC
2: 48010214 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
LRG_219t1:c.-159C>T
LRG_219:g.4929C>T
NC_000002.11:g.48010214C>T
... more HGVS
Protein change
-
Other names
-
Canonical SPDI
NC_000002.12:47783074:C:T
Functional consequence
-
Global minor allele frequency (GMAF)
0.02915 (T)

Allele frequency
Trans-Omics for Precision Medicine (TOPMed) 0.06435
1000 Genomes Project 0.02915
The Genome Aggregation Database (gnomAD) 0.08152
Links
ClinGen: CA330335
dbSNP: rs41540312
Varsome
Help

Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Benign 2 reviewed by expert panel Sep 5, 2013 RCV000074619.4
Benign 1 criteria provided, single submitter Jun 23, 2018 RCV001618241.3
Help
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
5639 5673

Submitted interpretations and evidence

Help
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: SCV000107871.2
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.
Likely benign
(Jun 14, 2016)
criteria provided, single submitter
Method: clinical testing
Lynch Syndrome
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV000483934.2
Submitted: (Oct 18, 2016)
Evidence details
Benign
(Jun 23, 2018)
criteria provided, single submitter
Method: clinical testing
Not Provided
Allele origin: germline
GeneDx
Accession: SCV001842689.1
Submitted: (Sep 09, 2021)
Evidence details

Functional evidence

Help
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

Help
Title Author Journal Year Link
http://www.insight-database.org/classifications/index.html?gene=MSH6&variant=c.-159C%3ET - - - -

Text-mined citations for rs41540312...

Help
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 Sep 29, 2021