ClinVar Miner

Submissions for variant NM_000535.7(PMS2):c.1708A>G (p.Asn570Asp) (rs115670442)

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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 RCV000129033 SCV000172943 likely benign Hereditary cancer-predisposing syndrome 2017-12-19 criteria provided, single submitter clinical testing Lines of evidence used in support of classification: In silico models in agreement (benign),Other data supporting benign classification
Color RCV000129033 SCV000910757 likely benign Hereditary cancer-predisposing syndrome 2016-02-25 criteria provided, single submitter clinical testing
GeneDx RCV000121841 SCV000279145 likely benign not specified 2017-10-11 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.
ITMI RCV000121841 SCV000086039 not provided not specified 2013-09-19 no assertion provided reference population
Integrated Genetics/Laboratory Corporation of America RCV000586004 SCV000697309 uncertain significance not provided 2016-09-16 criteria provided, single submitter clinical testing Variant summary: The PMS2 c.1708A>G (p.Asn570Asp) variant involves the alteration of a non-conserved nucleotide. This variant is not located in any known domain (InterPro). 5/5 in silico tools predict a benign outcome for this variant. This variant was found in 16/122394 control chromosomes, predominantly observed in the African subpopulation at a frequency of 0.0014663 (15/10230). This frequency is about 13 times the estimated maximal expected allele frequency of a pathogenic PMS2 variant (0.0001136), suggesting this is likely a benign polymorphism found primarily in the populations of African origin. However, there is high sequency homology in this region with PMS2 pseudogene, and control frequencies are based on technologies that cannot distinguish between the two, therefore caution must be taken with this data. Multiple clinical diagnostic laboratories have classified this variant as uncertain significance (2) to likely benign (1). The variant of interest has not, to our knowledge, been reported in affected individuals in literature, nor evaluated for functional impact by in vivo/vitro studies. Taken together, this variant is classified as VUS until additional evidence becomes available.
Invitae RCV000195850 SCV000253292 likely benign Hereditary nonpolyposis colon cancer 2018-01-16 criteria provided, single submitter clinical testing
Quest Diagnostics Nichols Institute San Juan Capistrano RCV000121841 SCV000601827 likely benign not specified 2017-07-05 criteria provided, single submitter clinical testing

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