ClinVar Miner

Submissions for variant NM_000535.7(PMS2):c.354-7C>T (rs758471869)

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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Color RCV000583777 SCV000691070 likely benign Hereditary cancer-predisposing syndrome 2017-09-16 criteria provided, single submitter clinical testing
Integrated Genetics/Laboratory Corporation of America RCV000590705 SCV000697363 uncertain significance not specified 2019-07-10 criteria provided, single submitter clinical testing Variant summary: PMS2 c.354-7C>T alters a non-conserved nucleotide located close to a canonical splice site and therefore could affect mRNA splicing, leading to a significantly altered protein sequence. 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 8e-06 in 251138 control chromosomes (gnomAD). The available data on variant occurrences in the general population are insufficient to allow any conclusion about variant significance. To our knowledge, no occurrence of c.354-7C>T in individuals affected with Lynch Syndrome and no experimental evidence demonstrating its impact on protein function have been reported. Two ClinVar submissions (evaluation after 2014) cite the variant as likely benign. Based on the evidence outlined above, the variant was classified as uncertain significance.
Counsyl RCV000662819 SCV000785662 likely benign Hereditary nonpolyposis colorectal cancer type 4 2017-10-23 criteria provided, single submitter clinical testing
Invitae RCV000868952 SCV001010337 likely benign Hereditary nonpolyposis colon cancer 2019-12-31 criteria provided, single submitter clinical testing

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