ClinVar Miner

Submissions for variant NM_000179.3(MSH6):c.3801+17T>C

gnomAD frequency: 0.00159  dbSNP: rs3136365
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Total submissions: 10
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000202209 SCV000170364 benign not specified 2014-03-14 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 RCV000411208 SCV000488085 likely benign Lynch syndrome 5 2015-12-22 criteria provided, single submitter clinical testing
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV000590707 SCV000695889 benign not provided 2016-01-04 criteria provided, single submitter clinical testing Variant summary: This c.3801+17T>C variant affects a non-conserved intronic nucleotide at a location not widely known to affect normal splicing. 5/5 splice-site tools via Alamut predict that this variant does not affect normal splicing. In addition, ESEfinder also predicts that this variant does not affect ESE sites. This variant is found in 51/10276 African control chromosomes (including 1 homozygote) at a frequency of 0.00496, which is about 34 times greater than the maximal expected frequency of a pathogenic allele (0.0001421) in this gene, suggesting this variant is benign. In addition, two clinical laboratories have classified this variant as benign/likely benign. Taken together, this variant was classified as Benign.
PreventionGenetics, part of Exact Sciences RCV000202209 SCV000805897 benign not specified 2017-06-07 criteria provided, single submitter clinical testing
Color Diagnostics, LLC DBA Color Health RCV000771088 SCV000902648 likely benign Hereditary cancer-predisposing syndrome 2015-04-23 criteria provided, single submitter clinical testing
Mendelics RCV000411208 SCV001135848 likely benign Lynch syndrome 5 2019-05-28 criteria provided, single submitter clinical testing
ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories RCV000202209 SCV001158693 benign not specified 2019-03-27 criteria provided, single submitter clinical testing
Labcorp Genetics (formerly Invitae), Labcorp RCV002055072 SCV002324037 benign Hereditary nonpolyposis colorectal neoplasms 2025-02-02 criteria provided, single submitter clinical testing
Ambry Genetics RCV000771088 SCV002622785 likely benign Hereditary cancer-predisposing syndrome 2015-10-21 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.
Mayo Clinic Laboratories, Mayo Clinic RCV000202209 SCV000257280 likely benign not specified no assertion criteria provided research

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