ClinVar Miner

Submissions for variant NM_000535.7(PMS2):c.830C>A (p.Thr277Lys) (rs1805322)

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Total submissions: 7
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Invitae RCV000123092 SCV000166392 benign Hereditary nonpolyposis colon cancer 2017-12-29 criteria provided, single submitter clinical testing
Ambry Genetics RCV000128979 SCV000172865 benign Hereditary cancer-predisposing syndrome 2014-11-18 criteria provided, single submitter clinical testing
GeneDx RCV000212851 SCV000211576 likely benign not specified 2018-01-19 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.
EGL Genetic Diagnostics,Eurofins Clinical Diagnostics RCV000586384 SCV000333805 uncertain significance not provided 2015-09-11 criteria provided, single submitter clinical testing
Color RCV000128979 SCV000686244 likely benign Hereditary cancer-predisposing syndrome 2015-09-23 criteria provided, single submitter clinical testing
Integrated Genetics/Laboratory Corporation of America RCV000586384 SCV000697389 benign not provided 2016-02-01 criteria provided, single submitter clinical testing Variant summary: The c.830C>A variant affects a conserved nucleotide, resulting in amino acid change from Thr to Lys. 3/4 in-silico tools predict this variant to be benign (SNPs&GO not captured due to low reliability index). 4/5 programs in Alamut predict that this variant does not affect normal splicing. ESE finder predicts that this variant may affect multiple ESE sites. However, these predictions are not confirmed by experimental studies. Sequence comparison suggests exon 8 does not match to any pseudogene region with high homology. This variant is found predominantly in African population at a frequency of 0.0045 (46/10332), which is about 39 times of maximal expected frequency of a pathogenic allele (0.0001136), suggesting this variant is benign. In addition, multiple clinical laboratories/literature classified this variant as benign. Taken together, this variant was classified as benign.
True Health Diagnostics RCV000128979 SCV000788120 likely benign Hereditary cancer-predisposing syndrome 2017-09-29 no assertion criteria provided clinical testing

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