ClinVar Miner

Submissions for variant NM_000179.3(MSH6):c.4001+2TAAC[4] (rs267608132)

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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 RCV000160734 SCV000186783 likely benign Hereditary cancer-predisposing syndrome 2013-03-21 criteria provided, single submitter clinical testing
GeneDx RCV000160734 SCV000211370 benign Hereditary cancer-predisposing syndrome 2014-02-17 criteria provided, single submitter clinical testing The variant is found in HEREDICANCER,BR-OV-HEREDIC panel(s).
Invitae RCV000204092 SCV000262244 likely benign not provided 2016-03-01 criteria provided, single submitter clinical testing
Counsyl RCV000409636 SCV000489203 likely benign Hereditary nonpolyposis colorectal cancer type 5 2016-09-07 criteria provided, single submitter clinical testing
Color RCV000160734 SCV000685476 likely benign Hereditary cancer-predisposing syndrome 2014-12-29 criteria provided, single submitter clinical testing
Integrated Genetics/Laboratory Corporation of America RCV000780481 SCV000917766 benign not specified 2018-06-07 criteria provided, single submitter clinical testing Variant summary: MSH6 c.4001+12_4001+15dupACTA alters a nucleotide located in the intronic region that is not widely known to affect splicing. 5/5 computational tools predict no significant impact on normal splicing. However, these predictions have yet to be confirmed by functional studies. The variant allele was found at a frequency of 0.00028 in 270198 control chromosomes. The observed variant frequency is approximately 2 fold above the estimated maximal expected allele frequency for a pathogenic variant in MSH6 causing Lynch Syndrome phenotype (0.00014), strongly suggesting that the variant is benign. To our knowledge, no occurrence of c.4001+12_4001+15dupACTA in individuals affected with Lynch Syndrome and no experimental evidence demonstrating its impact on protein function have been reported. Multiple clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar without evidence for independent evaluation. All laboratories classified the variant as benign/likely benign. Based on the evidence outlined above, the variant was classified as benign.
Mendelics RCV000409636 SCV001135858 likely benign Hereditary nonpolyposis colorectal cancer type 5 2019-05-28 criteria provided, single submitter clinical testing

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