ClinVar Miner

Submissions for variant NM_000179.3(MSH6):c.3255C>G (p.Thr1085=)

gnomAD frequency: 0.00001  dbSNP: rs371568610
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Total submissions: 9
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Ambry Genetics RCV000167307 SCV000218154 likely benign Hereditary cancer-predisposing syndrome 2014-12-12 criteria provided, single submitter clinical testing This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity.
Counsyl RCV000411260 SCV000488380 likely benign Lynch syndrome 5 2016-03-11 criteria provided, single submitter clinical testing
GeneDx RCV001721092 SCV000531748 likely benign not provided 2020-03-06 criteria provided, single submitter clinical testing
Invitae RCV000531634 SCV000624835 likely benign Hereditary nonpolyposis colorectal neoplasms 2023-11-24 criteria provided, single submitter clinical testing
Color Diagnostics, LLC DBA Color Health RCV000167307 SCV000685373 likely benign Hereditary cancer-predisposing syndrome 2016-08-19 criteria provided, single submitter clinical testing
Sema4, Sema4 RCV000167307 SCV002527992 likely benign Hereditary cancer-predisposing syndrome 2021-10-05 criteria provided, single submitter curation
Myriad Genetics, Inc. RCV000411260 SCV004018895 benign Lynch syndrome 5 2023-03-28 criteria provided, single submitter clinical testing This variant is considered benign. This variant is a silent/synonymous amino acid change and it is not expected to impact splicing.
All of Us Research Program, National Institutes of Health RCV003995580 SCV004835023 likely benign Lynch syndrome 2023-08-08 criteria provided, single submitter clinical testing
Department of Pathology and Laboratory Medicine, Sinai Health System RCV001353761 SCV000592630 likely benign Carcinoma of colon no assertion criteria provided clinical testing The MSH6, p.Thr1085Thr variant was identified only in dbSNP (ID: rs371568610) with a minor allele frequency of 0.0004 (1000 Genomes Project). It was not identified in NHLBI Exome Sequencing Project (Exome Variant Server), Exome Aggregation Consortium (ExAC) database, HGMD, COSMIC, MutDB, “Mismatch Repair Genes Variant Database”, “MMR Gene Unclassified Variants Database”, InSiGHT Colon Cancer Gene Variant Database, “Zhejiang Colon Cancer Database”, the ClinVar database, GeneInsight VariantWire database and UMD. The p.Thr1085Thr variant is not expected to have clinical significance because it does not result in a change of amino acid and is not located in a known consensus splice site. In addition, in silico or computational prediction software programs (SpliceSiteFinder, MaxEntScan, NNSPLICE, GeneSplicer, HumanSpliceFinder) do not predict a difference in splicing. In summary, based on the above information, the clinical significance of this variant cannot be determined with certainty at this time although we would lean towards a more benign role for this variant. This variant is classified as predicted benign.

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