ClinVar Miner

Submissions for variant NM_000535.7(PMS2):c.2049C>T (p.Asn683=) (rs752950007)

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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Ambry Genetics RCV000163909 SCV000214503 likely benign Hereditary cancer-predisposing syndrome 2014-06-03 criteria provided, single submitter clinical testing
Integrated Genetics/Laboratory Corporation of America RCV000780630 SCV000918061 uncertain significance not specified 2018-07-31 criteria provided, single submitter clinical testing Variant summary: PMS2 c.2049C>T alters a conserved nucleotide resulting in a synonymous change. 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 6.3e-05 in 239440 control chromosomes (gnomAD). This frequency is not significantly higher than expected for a pathogenic variant in PMS2 causing Lynch Syndrome (6.3e-05 vs 0.00011), allowing no conclusion about variant significance. To our knowledge, no occurrence of c.2049C>T in individuals affected with Lynch Syndrome and no experimental evidence demonstrating its impact on protein function have been reported. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014. Based on the evidence outlined above, the variant was classified as VUS-possibly benign.
Quest Diagnostics Nichols Institute San Juan Capistrano RCV000759918 SCV000889619 uncertain significance not provided 2018-01-10 criteria provided, single submitter clinical testing

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