ClinVar Miner

Submissions for variant NM_000179.2(MSH6):c.3960A>G (p.Ala1320=) (rs373425206)

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Total submissions: 7
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Ambry Genetics RCV000160731 SCV000213897 likely benign Hereditary cancer-predisposing syndrome 2014-07-31 criteria provided, single submitter clinical testing
Color RCV000160731 SCV000685468 likely benign Hereditary cancer-predisposing syndrome 2015-09-22 criteria provided, single submitter clinical testing
Counsyl RCV000409788 SCV000488676 likely benign Hereditary nonpolyposis colorectal cancer type 5 2016-05-20 criteria provided, single submitter clinical testing
GeneDx RCV000212692 SCV000211366 benign not specified 2014-08-29 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.
Integrated Genetics/Laboratory Corporation of America RCV000212692 SCV000917749 likely benign not specified 2018-01-08 criteria provided, single submitter clinical testing Variant summary: The MSH6 c.3960A>G (p.Ala1320Ala) variant involves the alteration of a non-conserved nucleotide, resulting in a synonymous change. Mutation taster 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 not affect binding of ESE sites. However, these predictions have yet to be confirmed by functional studies. This variant was found in 31/274432 control chromosomes, predominantly observed in the African subpopulation at a frequency of 0.001172 (28/23886). This frequency is about 8 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 benign/likely benign. The variant of interest has not, to our knowledge, been reported in affected individuals via publications. Taken together, this variant is classified as likely benign.
Invitae RCV000205020 SCV000261398 benign Hereditary nonpolyposis colon cancer 2017-12-27 criteria provided, single submitter clinical testing
True Health Diagnostics RCV000160731 SCV000788054 likely benign Hereditary cancer-predisposing syndrome 2017-10-10 no assertion criteria provided clinical testing

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