ClinVar Miner

Submissions for variant NM_000535.7(PMS2):c.2007-7C>T

gnomAD frequency: 0.12135  dbSNP: rs55954143
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Total submissions: 19
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
International Society for Gastrointestinal Hereditary Tumours (InSiGHT) RCV000030366 SCV000108331 no known pathogenicity Lynch syndrome 2013-09-05 reviewed by expert panel research MAF >1%
Eurofins Ntd Llc (ga) RCV000153747 SCV000203314 benign not specified 2018-03-21 criteria provided, single submitter clinical testing
Invitae RCV000857365 SCV000252714 benign Hereditary nonpolyposis colorectal neoplasms 2024-02-01 criteria provided, single submitter clinical testing
Preventiongenetics, part of Exact Sciences RCV000153747 SCV000304728 benign not specified criteria provided, single submitter clinical testing
Illumina Laboratory Services, Illumina RCV000625383 SCV000469719 benign Lynch syndrome 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 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 RCV001668144 SCV000604894 benign not provided 2023-10-23 criteria provided, single submitter clinical testing
Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center RCV000625383 SCV000745186 benign Lynch syndrome 4 2017-05-31 criteria provided, single submitter clinical testing
Counsyl RCV000625383 SCV000785198 benign Lynch syndrome 4 2017-06-13 criteria provided, single submitter clinical testing
GeneDx RCV001668144 SCV001891188 benign not provided 2015-03-03 criteria provided, single submitter clinical testing
Ambry Genetics RCV002415437 SCV002719549 benign Hereditary cancer-predisposing syndrome 2014-09-15 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.
KCCC/NGS Laboratory, Kuwait Cancer Control Center RCV000625383 SCV004016581 benign Lynch syndrome 4 2023-07-07 criteria provided, single submitter clinical testing
Myriad Genetics, Inc. RCV000625383 SCV004019871 benign Lynch syndrome 4 2023-04-05 criteria provided, single submitter clinical testing This variant is considered benign. This variant is intronic and is not expected to impact mRNA splicing.
Color Diagnostics, LLC DBA Color Health RCV002415437 SCV004359576 benign Hereditary cancer-predisposing syndrome 2015-03-31 criteria provided, single submitter clinical testing
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV000030366 SCV000053033 benign Lynch syndrome 2013-12-27 no assertion criteria provided clinical testing
Department of Pathology and Laboratory Medicine, Sinai Health System RCV001353925 SCV000592943 benign Endometrial carcinoma no assertion criteria provided clinical testing The PMS2 c.2007-7C>T variant was identified in 24 of 1372 proband chromosomes (frequency: 0.017) from individuals or families with Lynch syndrome, but was classified as a benign polymorphism (Hansen 2014, Hendriks 2006, Niessen 2009, Sheng 2010, van der Klift 2016). The variant was also identified in dbSNP (rs55954143) with benign allele, ClinVar 6x (classified as benign, reviewed by an expert panel), Genesight-COGR, Insight Colon Cancer Gene Variant Database (as benign), and Mismatch Repair Genes Variant Database. The variant was not identified in Cosmic, MutDB, Zhejiang Colon Cancer Database, MMR Gene Unclassified Variants Database, or Insight Hereditary Tumors Database. The variant was identified in control databases in 14684 of 174456 chromosomes (776 homozygous) at a frequency of 0.08 increasing the likelihood this could be a low frequency benign variant (Genome Aggregation Consortium Feb 27, 2017). The variant was identified in the following populations at a frequency greater than 1%: African in 3950 of 15996 chromosomes (freq: 0.247), East Asian in 1045 of 11848 chromosomes (freq: 0.088), European (Finnish) in 1617 of 19226 chromosomes (freq: 0.084), South Asian in 1722 of 20892 chromosomes (freq: 0.082), Other in 326 of 4640 chromosomes (freq: 0.07), European (Non-Finnish) in 4958 of 72394 chromosomes (freq: 0.068), Ashkenazi Jewish* in 329 of 7828 chromosomes (freq: 0.042). In summary, based on the above information this variant meets our laboratory's criteria to be classified as benign.
Mayo Clinic Laboratories, Mayo Clinic RCV000153747 SCV000691963 benign not specified no assertion criteria provided clinical testing
Clinical Genetics Laboratory, Department of Pathology, Netherlands Cancer Institute RCV000153747 SCV001905926 benign not specified no assertion criteria provided clinical testing
Clinical Genetics, Academic Medical Center RCV000153747 SCV001921665 benign not specified no assertion criteria provided clinical testing
Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+ RCV000153747 SCV001953515 benign not specified no assertion criteria provided clinical testing

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