ClinVar Miner

Submissions for variant NM_000535.7(PMS2):c.353+9A>C (rs139990791)

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Total submissions: 8
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000127471 SCV000171044 benign not specified 2014-05-23 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.
Invitae RCV000206775 SCV000260021 benign Hereditary nonpolyposis colon cancer 2017-12-27 criteria provided, single submitter clinical testing
Counsyl RCV000410849 SCV000487936 likely benign Hereditary nonpolyposis colorectal cancer type 4 2015-12-04 criteria provided, single submitter clinical testing
Genetic Services Laboratory, University of Chicago RCV000127471 SCV000596474 likely benign not specified 2016-01-12 criteria provided, single submitter clinical testing
Color RCV000580954 SCV000686194 likely benign Hereditary cancer-predisposing syndrome 2015-10-09 criteria provided, single submitter clinical testing
Integrated Genetics/Laboratory Corporation of America RCV000588382 SCV000697362 benign not provided 2017-08-16 criteria provided, single submitter clinical testing Variant summary: The PMS2 c.353+9A>C variant involves the alteration of a non-conserved intronic nucleotideand 5/5 splice prediction tools predict no significant impact on normal splicing. However, these predictions have yet to be confirmed by functional studies. This variant was found in 70/260874 control chromosomes, predominantly observed in the African subpopulation at a frequency of 0.002958 (67/22652). This frequency is about 26 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. In addition, multiple clinical diagnostic laboratories classified this variant as "likely benign/benign." The variant of interest has not, to our knowledge, been reported in affected individuals via publications. Taken together, this variant is classified as benign.
PreventionGenetics,PreventionGenetics RCV000127471 SCV000806216 benign not specified 2016-12-30 criteria provided, single submitter clinical testing
EGL Genetic Diagnostics,Eurofins Clinical Diagnostics RCV000127471 SCV000861357 likely benign not specified 2018-05-29 criteria provided, single submitter clinical testing

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