ClinVar Miner

Submissions for variant NM_000179.2(MSH6):c.3151G>A (p.Val1051Ile) (rs576269342)

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Total submissions: 7
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Invitae RCV000122961 SCV000166225 benign Hereditary nonpolyposis colon cancer 2017-12-14 criteria provided, single submitter clinical testing
Ambry Genetics RCV000132157 SCV000187231 uncertain significance Hereditary cancer-predisposing syndrome 2017-08-10 criteria provided, single submitter clinical testing Lines of evidence used in support of classification: Insufficient or conflicting evidence,In silico models in agreement (benign)
GeneDx RCV000235186 SCV000211312 likely benign not specified 2018-01-04 criteria provided, single submitter clinical testing This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease.
Counsyl RCV000408980 SCV000488006 uncertain significance Hereditary nonpolyposis colorectal cancer type 5 2015-12-11 criteria provided, single submitter clinical testing
Integrated Genetics/Laboratory Corporation of America RCV000588824 SCV000695839 benign not provided 2016-04-29 criteria provided, single submitter clinical testing Variant summary: The variant of interest causes a missense change involving a conserved nucleotide with 4/5 in silico programs predicting a "benign" outcome, although these predictions have yet to be functionally assessed. The variant of interest was observed in the large, broad control population, ExAC, with an allele frequency of 107/119266 (1/1114), predominantly in the South Asian cohort, 106/16430 (1/154), which exceeds the predicted maximum expected allele frequency for a pathogenic MSH6 variant of 1/7037. Therefore, suggesting that the variant of interest is a common polymorphism found in population(s) of South Asian origin. The variant of interest was observed in affected individuals via a publication, although with limited information (ie lack of co-occurrence/co-segregation data). Multiple reputable clinical laboratories cite the variant with a classification of "uncertain significance," however, it should be noted that these classifications were evaluated previous to ExAC data being available. Therefore, taking all available lines of evidence into consideration, the variant of interest is classified as Benign.
PreventionGenetics,PreventionGenetics RCV000588824 SCV000805875 uncertain significance not provided 2017-01-06 criteria provided, single submitter clinical testing
Color RCV000132157 SCV000902696 benign Hereditary cancer-predisposing syndrome 2016-05-12 criteria provided, single submitter clinical testing

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