ClinVar Miner

Submissions for variant NM_000535.7(PMS2):c.23+10G>C (rs192027828)

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Total submissions: 16
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Invitae RCV000119180 SCV000153913 benign Hereditary nonpolyposis colorectal neoplasms 2020-12-04 criteria provided, single submitter clinical testing
GeneDx RCV000212835 SCV000171045 benign not specified 2013-12-17 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 RCV000130558 SCV000185428 benign Hereditary cancer-predisposing syndrome 2014-11-18 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.
Counsyl RCV000409370 SCV000489257 likely benign Hereditary nonpolyposis colorectal cancer type 4 2016-09-08 criteria provided, single submitter clinical testing
Genetic Services Laboratory, University of Chicago RCV000212835 SCV000596475 likely benign not specified 2016-08-16 criteria provided, single submitter clinical testing
Color Health, Inc RCV000130558 SCV000686179 likely benign Hereditary cancer-predisposing syndrome 2015-04-01 criteria provided, single submitter clinical testing
Genome Diagnostics Laboratory, University Medical Center Utrecht RCV000409370 SCV000743787 likely benign Hereditary nonpolyposis colorectal cancer type 4 2016-02-05 criteria provided, single submitter clinical testing
Genome Diagnostics Laboratory, Amsterdam University Medical Center RCV000409370 SCV000745851 likely benign Hereditary nonpolyposis colorectal cancer type 4 2016-07-11 criteria provided, single submitter clinical testing
PreventionGenetics,PreventionGenetics RCV000212835 SCV000806203 benign not specified 2017-02-24 criteria provided, single submitter clinical testing
ARUP Laboratories, Molecular Genetics and Genomics,ARUP Laboratories RCV001282885 SCV001158630 benign none provided 2020-07-04 criteria provided, single submitter clinical testing
Illumina Clinical Services Laboratory,Illumina RCV000409370 SCV001322571 benign Hereditary nonpolyposis colorectal cancer type 4 2017-04-27 criteria provided, single submitter clinical testing This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). Publications were found based on this search. The evidence from the literature, in combination with allele frequency data from public databases where available, was sufficient to rule this variant out of causing disease. Therefore, this variant is classified as benign.
Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen RCV000409370 SCV000734571 likely benign Hereditary nonpolyposis colorectal cancer type 4 no assertion criteria provided clinical testing
Department of Pathology and Laboratory Medicine,Sinai Health System RCV000212835 SCV001553285 benign not specified no assertion criteria provided clinical testing The PMS2 c.23+10G>C variant was not identified in the literature nor was it identified in the following databases: COGR, Clinvitae, Cosmic, MutDB, Insight Colon Cancer Gene Variant Database, Zhejiang Colon Cancer Database, Mismatch Repair Genes Variant Database, or the Insight Hereditary Tumors Database. The variant was identified in dbSNP (ID: rs192027828) “With other allele”, ClinVar (classified benign by Invitae, GeneDx and Ambry Genetics; and likely benign by Counsyl and Genetic Services Laboratory (University of Chicago)), and in control databases in 496 (2 homozygous) of 276428 chromosomes at a frequency of 0.002 increasing the likelihood this could be a low frequency variant in certain populations (Genome Aggregation Consortium Feb 27, 2017). It was observed in the following populations: African in 16 of 23946 chromosomes (freq. 0.0007), other in 10 of 6460 chromosomes (freq. 0.002), Latino in 31 of 34414 chromosomes (freq. 0.0009), European Non-Finnish in 365 (2 homozygous) of 126042 chromosomes (freq. 0.003), Ashkenazi Jewish in 1 of 10138 chromosomes (freq:0.0001), European Finnish in 42 of 25794 chromosomes (freq:0.002) and South Asian in 31 of 30776 chromosomes (freq. 0.001); it was not seen in the East Asian population. The variant occurs outside of the splicing consensus sequence and in silico or computational prediction software programs (SpliceSiteFinder, MaxEntScan, NNSPLICE, GeneSplicer, HumanSpliceFinder) do not predict a difference in splicing. In summary, based on the above information this variant meets our laboratory's criteria to be classified as benign.
Clinical Genetics Laboratory, Department of Pathology,Netherlands Cancer Institute RCV001705879 SCV001905843 likely benign not provided no assertion criteria provided clinical testing
Clinical Genetics,Academic Medical Center RCV000212835 SCV001925477 benign not specified no assertion criteria provided clinical testing
Human Genetics - Radboudumc,Radboudumc RCV001705879 SCV001958167 likely benign not provided no assertion criteria provided clinical testing

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