ClinVar Miner

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

Minimum review status: Collection method:
Minimum conflict level:
ClinVar version:
Total submissions: 6
Download table as spreadsheet
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
Invitae RCV000206607 SCV000260101 likely benign Hereditary nonpolyposis colon cancer 2017-12-16 criteria provided, single submitter clinical testing
GeneDx RCV000427063 SCV000529717 likely benign not specified 2017-03-09 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.
Color RCV000164429 SCV000685198 likely benign Hereditary cancer-predisposing syndrome 2015-12-10 criteria provided, single submitter clinical testing
Integrated Genetics/Laboratory Corporation of America 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

The information on this website is not intended for direct diagnostic use or medical decision-making without review by a genetics professional. Individuals should not change their health behavior solely on the basis of information contained on this website. Neither the University of Utah nor the National Institutes of Health independently verfies the submitted information. If you have questions about the information contained on this website, please see a health care professional.