ClinVar Miner

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

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Total submissions: 4
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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
Quest Diagnostics Nichols Institute San Juan Capistrano RCV000759918 SCV000889619 uncertain significance not provided 2018-01-10 criteria provided, single submitter clinical testing
Integrated Genetics/Laboratory Corporation of America RCV000780630 SCV000918061 likely benign not specified 2019-03-12 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. 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. One laboratory in ClinVar has classified the variant as likely benign in 2014. Based upon our independent evaluation, no additional evidence supporting a pathogenic outcome have emerged between 2014 to present. Based on the evidence outlined above, the variant was classified as likely benign.
Invitae RCV001082995 SCV001009179 likely benign Hereditary nonpolyposis colon cancer 2019-12-31 criteria provided, single submitter clinical testing

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