ClinVar Miner

Submissions for variant NM_000535.7(PMS2):c.1560G>A (p.Ala520=) (rs201167814)

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Total submissions: 9
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000127461 SCV000171028 benign not specified 2014-01-22 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.
Ambry Genetics RCV000162432 SCV000212779 likely benign Hereditary cancer-predisposing syndrome 2014-05-23 criteria provided, single submitter clinical testing
Invitae RCV001079708 SCV000253288 benign Hereditary nonpolyposis colon cancer 2019-12-30 criteria provided, single submitter clinical testing
Color RCV000162432 SCV000537477 likely benign Hereditary cancer-predisposing syndrome 2015-06-15 criteria provided, single submitter clinical testing
CeGaT Praxis fuer Humangenetik Tuebingen RCV000487654 SCV000575509 likely benign not provided 2019-05-01 criteria provided, single submitter clinical testing
Integrated Genetics/Laboratory Corporation of America RCV000487654 SCV000697302 benign not provided 2017-06-26 criteria provided, single submitter clinical testing Variant summary: The c.1560G>A (p.Ala520=) in PMS2 gene is a synonymous change that involves a non-conserved nucleotide. 4/5 programs in Alamut predict that this variant does not affect the normal splicing, however no functional studies supporting this notion were published at the time of evaluation. The variant is present in the control population datasets of ExAC and gnomAD at a similar frequencies 0.00033 (38/120402 and 93/277018 chrs tested, respectively), which is about 3 times of the maximum expected allele frequency for a pathogenic PMS2 variant (0.00011). Sequence allignment and reads in ExAC support that the minor alleles reported in ExAC are not from the pseudogene. The variant has not, to our knowledge, been reported in affected individuals via published reports but is cited as Benign/Likely Benign by reputable databases/clinical laboratories. Taking together, the variant was classified as benign.
Quest Diagnostics Nichols Institute San Juan Capistrano RCV000487654 SCV000888395 benign not provided 2019-03-22 criteria provided, single submitter clinical testing
Illumina Clinical Services Laboratory,Illumina RCV001159293 SCV001320993 uncertain significance Hereditary nonpolyposis colorectal cancer type 4 2018-01-12 criteria provided, single submitter clinical testing This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score, this variant could not be ruled out of causing disease and therefore its association with disease required further investigation. A literature search was performed for the gene, cDNA change, and amino acid change (if applicable). No publications were found based on this search. This variant was therefore classified as a variant of unknown significance for this disease.
True Health Diagnostics RCV000162432 SCV000788106 likely benign Hereditary cancer-predisposing syndrome 2017-09-27 no assertion criteria provided clinical testing

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