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NM_000179.2(MSH6):c.3537C>G (p.Ala1179=)

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Interpretation:
Conflicting interpretations of pathogenicity​

Likely benign(2);Uncertain significance(1)

Review status:
criteria provided, conflicting interpretations
Submissions:
3 (Most recent: Jan 7, 2021)
Last evaluated:
Oct 29, 2020
Accession:
VCV000185718.7
Variation ID:
185718
Description:
single nucleotide variant
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NM_000179.2(MSH6):c.3537C>G (p.Ala1179=)

Allele ID
182166
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
2p16.3
Genomic location
2: 47805008 (GRCh38) GRCh38 UCSC
2: 48032147 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000002.11:g.48032147C>G
NC_000002.12:g.47805008C>G
NM_000179.2:c.3537C>G NP_000170.1:p.Ala1179= synonymous
... more HGVS
Protein change
-
Other names
-
Canonical SPDI
NC_000002.12:47805007:C:G
Functional consequence
-
Global minor allele frequency (GMAF)
0.00020 (G)

Allele frequency
Trans-Omics for Precision Medicine (TOPMed) 0.00001
Exome Aggregation Consortium (ExAC) 0.00007
The Genome Aggregation Database (gnomAD), exomes 0.00004
1000 Genomes Project 0.00020
Links
ClinGen: CA013308
dbSNP: rs200120044
Varsome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Likely benign 1 criteria provided, single submitter Oct 29, 2020 RCV000629711.4
Conflicting interpretations of pathogenicity 2 criteria provided, conflicting interpretations Sep 16, 2019 RCV000165194.2
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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
5630 5664

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Likely benign
(Aug 01, 2014)
criteria provided, single submitter
Method: clinical testing
Hereditary cancer-predisposing syndrome
Allele origin: germline
Ambry Genetics
Accession: SCV000215906.5
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
(Sep 16, 2019)
criteria provided, single submitter
Method: clinical testing
Hereditary cancer-predisposing syndrome
Allele origin: germline
Color Health, Inc
Accession: SCV001354177.1
Submitted: (May 19, 2020)
Comment:
This variant causes a C>G nucleotide substitution in exon 6 of the MSH6 gene. Splice site prediction tools suggest that this variant activates a cryptic … (more)
Evidence details
Likely benign
(Oct 29, 2020)
criteria provided, single submitter
Method: clinical testing
Hereditary nonpolyposis colorectal neoplasms
Allele origin: germline
Invitae
Accession: SCV000750667.4
Submitted: (Jan 07, 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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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 rs200120044...

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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 Feb 03, 2021