ClinVar Miner

Submissions for variant NM_000535.6(PMS2):c.1320A>G (p.Pro440=) (rs138697590)

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Total submissions: 7
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Ambry Genetics RCV000162674 SCV000213121 likely benign Hereditary cancer-predisposing syndrome 2014-09-17 criteria provided, single submitter clinical testing
Color RCV000162674 SCV000537450 likely benign Hereditary cancer-predisposing syndrome 2015-04-27 criteria provided, single submitter clinical testing
GeneDx RCV000127460 SCV000171025 benign not specified 2014-03-18 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.
Integrated Genetics/Laboratory Corporation of America RCV000588011 SCV000697293 uncertain significance not provided 2016-11-25 criteria provided, single submitter clinical testing Variant summary: The PMS2 c.1320A>G (p.Pro440Pro) variant causes a synonymous change involving a non-conserved nucleotide, which 4/5 splice prediction tools predict no significant impact on normal splicing and ESE finder predicts alterations to ESE binding, however, these predictions have yet to be functionally assessed. The variant of interest has been observed in the large, broad control population, ExAC, with an allele frequency of 4/120980 (1/30211), which does not exceed the estimated maximal expected allele frequency for a pathogenic PMS2 variant of 1/8802. The variant of interest has not, to our knowledge, been reported in affected individuals via publications, however, multiple clinical diagnostic laboratories cite the variant with a classification of "likely benign/benign." Therefore, the variant of interest has been classified as a "Variant of Uncertain Significance - Possibly Benign."
Invitae RCV000123074 SCV000166369 likely benign Hereditary nonpolyposis colon cancer 2017-12-05 criteria provided, single submitter clinical testing
Quest Diagnostics Nichols Institute San Juan Capistrano RCV000127460 SCV000601814 likely benign not specified 2017-06-23 criteria provided, single submitter clinical testing
Quest Diagnostics Nichols Institute San Juan Capistrano RCV000588011 SCV000888389 likely benign not provided 2017-06-23 criteria provided, single submitter clinical testing

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