ClinVar Miner

Submissions for variant NM_000179.2(MSH6):c.3647-6T>A (rs182871847)

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Total submissions: 8
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Color RCV000579665 SCV000685425 likely benign Hereditary cancer-predisposing syndrome 2015-04-07 criteria provided, single submitter clinical testing
Counsyl RCV000662552 SCV000785135 likely benign Hereditary nonpolyposis colorectal cancer type 5 2017-05-04 criteria provided, single submitter clinical testing
GeneDx RCV000115418 SCV000149327 likely benign not specified 2017-09-28 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.
Genetic Services Laboratory, University of Chicago RCV000115418 SCV000595843 uncertain significance not specified 2016-09-08 criteria provided, single submitter clinical testing
Integrated Genetics/Laboratory Corporation of America RCV000587059 SCV000695881 benign not provided 2016-10-06 criteria provided, single submitter clinical testing Variant summary: The MSH6 c.3647-6T>A variant involves the alteration of a non-conserved intronic nucleotide with 4/5 splice prediction tools predict no significant impact on normal splicing, which a reputable database reports in vitro and ex vivo analyses that support these predictions. The variant of interest was observed in the large, broad control population, ExAC, with an allele frequency of 47/120200 (1/2557), predominantly in the African cohort, 42/10262 (1/244), which exceeds the estimated maximal expected allele frequency for a pathogenic MSH6 variant of 1/7037. Therefore, suggesting this is likely a benign polymorphism found primarily in population(s) of African origin. The variant of interest has been reported by multiple clinical diagnostic laboratories/databases with conflicting classifications "Benign/Likely Benign/Uncertain Significance." Therefore, taking all available lines of evidence into consideration, the variant of interest has been classified as Benign.
Invitae RCV000197774 SCV000252629 benign Hereditary nonpolyposis colon cancer 2018-01-09 criteria provided, single submitter clinical testing
Quest Diagnostics Nichols Institute San Juan Capistrano RCV000115418 SCV000601581 benign not specified 2016-11-28 criteria provided, single submitter clinical testing
True Health Diagnostics RCV000579665 SCV000788051 uncertain significance Hereditary cancer-predisposing syndrome 2018-02-20 no assertion criteria provided clinical testing

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