ClinVar Miner

Submissions for variant NM_000535.7(PMS2):c.2570G>C (p.Gly857Ala) (rs1802683)

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Total submissions: 15
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
International Society for Gastrointestinal Hereditary Tumours (InSiGHT) RCV000030370 SCV000108358 no known pathogenicity Lynch syndrome 2013-09-05 reviewed by expert panel research MAF >1%
EGL Genetic Diagnostics, Eurofins Clinical Diagnostics RCV000079109 SCV000110978 benign not specified 2018-04-05 criteria provided, single submitter clinical testing
Ambry Genetics RCV000130363 SCV000185215 benign Hereditary cancer-predisposing syndrome 2014-10-22 criteria provided, single submitter clinical testing This alteration is classified as benign based on a combination of the following: population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity.
Invitae RCV001079827 SCV000252720 benign Hereditary nonpolyposis colorectal neoplasms 2020-11-30 criteria provided, single submitter clinical testing
PreventionGenetics,PreventionGenetics RCV000079109 SCV000304733 benign not specified criteria provided, single submitter clinical testing
Illumina Clinical Services Laboratory,Illumina RCV000625382 SCV000469714 benign Hereditary nonpolyposis colorectal cancer type 4 2018-01-13 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 and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease.
ARUP Laboratories, Molecular Genetics and Genomics,ARUP Laboratories RCV001282050 SCV000604890 benign none provided 2020-09-01 criteria provided, single submitter clinical testing
DNA and Cytogenetics Diagnostics Unit,Erasmus Medical Center RCV000625382 SCV000745183 benign Hereditary nonpolyposis colorectal cancer type 4 2015-09-21 criteria provided, single submitter clinical testing
Counsyl RCV000625382 SCV000785321 benign Hereditary nonpolyposis colorectal cancer type 4 2017-07-06 criteria provided, single submitter clinical testing
Mendelics RCV000625382 SCV001137275 benign Hereditary nonpolyposis colorectal cancer type 4 2019-05-28 criteria provided, single submitter clinical testing
Biesecker Lab/Clinical Genomics Section,National Institutes of Health RCV000034628 SCV000043413 no known pathogenicity not provided 2012-07-13 no assertion criteria provided research Converted during submission to Benign.
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV000030370 SCV000053037 benign Lynch syndrome 2013-11-20 no assertion criteria provided clinical testing
Pathway Genomics RCV000144646 SCV000189973 benign Lynch syndrome I 2014-07-24 no assertion criteria provided clinical testing
Department of Pathology and Laboratory Medicine,Sinai Health System RCV001353501 SCV000592955 benign Endometrial carcinoma no assertion criteria provided clinical testing The PMS2 p.Gly857Ala variant was identified in 28% of 213820 control alleles in the Genome Aggregation Consortium (February 27, 2017). According to ACMG guidelines for variant classification based on allele frequency, category BA1, this variant is considered benign and has not been further reviewed (Richards 2015).”
Mayo Clinic Laboratories, Mayo Clinic RCV000079109 SCV000691955 benign not specified no assertion criteria provided clinical testing

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