ClinVar Miner

Submissions for variant NM_000179.2(MSH6):c.4001+1G>C (rs1114167729)

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Total submissions: 2
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Ambry Genetics RCV000490987 SCV000580199 likely pathogenic Hereditary cancer-predisposing syndrome 2015-01-19 criteria provided, single submitter clinical testing
Integrated Genetics/Laboratory Corporation of America RCV000588908 SCV000695908 likely pathogenic Lynch syndrome 2017-07-20 criteria provided, single submitter clinical testing Variant summary: The c.4001+1G>C (aka IVS9+1G>C) in a MSH6 gene is a splice-site variant that alters a highly conserved nucleotide. 5/5 in silico tools via Alamut predict this variant to eliminate a canonical donor sequence, however these predictions have yet to be confirmed by functional assay. The variant is absent from control datasets of ExAC and gnomAD (112936 and 270198 chrs tested, respectively). The variant has not, to our knowledge, been reported in affected individuals via publications, but is cited as Likely Pathogenic by a reputable database/clinical laboratory. In addition, two other alterations of the same nucleotide, c.4001+1G>A and c.4001+1G>T have been reported as casual in patients with CRC. Taken together, the variant was classified as Likely Pathogenic until additional information becomes available.

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