ClinVar Miner

Submissions for variant NM_000179.2(MSH6):c.1509C>T (p.Ser503=) (rs545020313)

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Total submissions: 6
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Ambry Genetics RCV000164429 SCV000215068 likely benign Hereditary cancer-predisposing syndrome 2014-05-28 criteria provided, single submitter clinical testing 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, 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.
Invitae RCV001087955 SCV000260101 likely benign Hereditary nonpolyposis colorectal neoplasms 2020-11-16 criteria provided, single submitter clinical testing
GeneDx RCV000586304 SCV000529717 likely benign not provided 2020-11-12 criteria provided, single submitter clinical testing
Color Health, Inc RCV000164429 SCV000685198 likely benign Hereditary cancer-predisposing syndrome 2015-12-10 criteria provided, single submitter clinical testing
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV000586304 SCV000695786 likely benign not provided 2016-08-16 criteria provided, single submitter clinical testing Variant summary: The MSH6 c.1509C>T (p.Ser503Ser) variant involves the alteration of a non-conserved nucleotide, resulting in a synonymous change. One in silico tool predicts a damaging outcome for this variant. 5/5 splice prediction tools predict no significant impact on normal splicing. ESE finder predicts that this variant may create a novel ESE site of SRp55. However, these predictions have yet to be confirmed by functional studies. This variant was found in 6/121298 control chromosomes, predominantly observed in the African subpopulation at a frequency of 0.0005767 (6/10404). This frequency is about 4 times the estimated maximal expected allele frequency of a pathogenic MSH6 variant (0.0001421), suggesting this is likely a benign polymorphism found primarily in the populations of African origin. In addition, multiple clinical diagnostic laboratories/reputable databases classified this variant as likely benign. The variant of interest has not, to our knowledge, been reported in affected individuals via publications and/or reputable databases/clinical diagnostic laboratories; nor evaluated for functional impact by in vivo/vitro studies. Taken together, this variant is classified as likely benign.
Quest Diagnostics Nichols Institute San Juan Capistrano RCV000586304 SCV000888242 benign not provided 2018-07-19 criteria provided, single submitter clinical testing

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