ClinVar Miner

Submissions for variant NM_000535.7(PMS2):c.23+7G>C (rs878854047)

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Total submissions: 5
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000423172 SCV000521985 likely benign not specified 2016-12-21 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.
Invitae RCV001088041 SCV000562215 likely benign Hereditary nonpolyposis colon cancer 2019-12-31 criteria provided, single submitter clinical testing
Quest Diagnostics Nichols Institute San Juan Capistrano RCV000759200 SCV000888405 likely benign not provided 2017-09-28 criteria provided, single submitter clinical testing
Color RCV000775888 SCV000910368 likely benign Hereditary cancer-predisposing syndrome 2018-08-21 criteria provided, single submitter clinical testing
Integrated Genetics/Laboratory Corporation of America RCV000423172 SCV000920025 uncertain significance not specified 2018-01-16 criteria provided, single submitter clinical testing Variant summary: The PMS2 c.23+7G>C variant involves the alteration of a non-conserved intronic nucleotide. One in silico tool predicts a benign outcome for this variant. 5/5 splice prediction tools predict no significant impact on normal splicing. However, these predictions have yet to be confirmed by functional studies. This variant was found in 4/245438 control chromosomes, predominantly observed in the South Asian subpopulation at a frequency of 0.000097 (3/30780). Though this frequency is near to the estimated maximal expected allele frequency of a pathogenic PMS2 variant (0.0001136), the technology utilized for the gnomAD dataset does not rule out pseudogene interference, thus this data cannot be relied upon. The variant of interest has not, to our knowledge, been reported in affected individuals via publications. In addition, multiple clinical diagnostic laboratories/reputable databases classified this variant as likely benign. Because of the absence of clinical information and the lack of functional studies, the variant is classified as a variant of uncertain significance (VUS)-possibly benign, until additional information becomes available.

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