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NM_000179.2(MSH6):c.1740G>T (p.Ser580=)

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Interpretation:
Conflicting interpretations of pathogenicity​

Likely benign(1);Uncertain significance(2)

Review status:
criteria provided, conflicting interpretations
Submissions:
3 (Most recent: Nov 30, 2020)
Last evaluated:
Aug 21, 2019
Accession:
VCV000216301.5
Variation ID:
216301
Description:
single nucleotide variant
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NM_000179.2(MSH6):c.1740G>T (p.Ser580=)

Allele ID
212237
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
2p16.3
Genomic location
2: 47799723 (GRCh38) GRCh38 UCSC
2: 48026862 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
LRG_219:g.21577G>T
NC_000002.11:g.48026862G>T
NC_000002.12:g.47799723G>T
... more HGVS
Protein change
-
Other names
-
Canonical SPDI
NC_000002.12:47799722:G:T
Functional consequence
-
Global minor allele frequency (GMAF)
-

Allele frequency
-
Links
ClinGen: CA068098
dbSNP: rs762089407
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 Aug 11, 2017 RCV000198145.3
Conflicting interpretations of pathogenicity 2 criteria provided, conflicting interpretations Aug 21, 2019 RCV000579551.4
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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
Uncertain significance
(Aug 11, 2017)
criteria provided, single submitter
Method: clinical testing
Hereditary nonpolyposis colorectal neoplasms
Allele origin: germline
Invitae
Accession: SCV000254281.4
Submitted: (Apr 02, 2018)
Evidence details
Comment:
This sequence change affects codon 580 of the MSH6 mRNA. It is a 'silent' change, meaning that it does not change the encoded amino acid … (more)
Uncertain significance
(Aug 21, 2019)
criteria provided, single submitter
Method: clinical testing
Hereditary cancer-predisposing syndrome
Allele origin: germline
Color Health, Inc
Accession: SCV000685224.3
Submitted: (May 19, 2020)
Comment:
This synonymous variant does not change the amino acid sequence of the MSH6 protein. Splice site prediction tools suggest that this variant may create a … (more)
Evidence details
Likely benign
(Jun 04, 2019)
criteria provided, single submitter
Method: clinical testing
Hereditary cancer-predisposing syndrome
Allele origin: germline
Ambry Genetics
Accession: SCV001173435.2
Submitted: (Nov 30, 2020)
Evidence details
Comment:
In silico models in agreement (benign);Synonymous alterations with insufficient evidence to classify as benign

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 rs762089407...

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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