ClinVar Miner

Submissions for variant NM_152564.5(VPS13B):c.6455-4dup

dbSNP: rs398124337
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Total submissions: 6
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Eurofins Ntd Llc (ga) RCV000081908 SCV000113843 benign not specified 2013-03-11 criteria provided, single submitter clinical testing
Illumina Laboratory Services, Illumina RCV000371009 SCV000470819 likely benign Cohen syndrome 2016-06-14 criteria provided, single submitter clinical testing
Ambry Genetics RCV002311684 SCV000847181 benign Inborn genetic diseases 2017-05-15 criteria provided, single submitter clinical testing This alteration is classified as benign based on a combination of the following: seen in unaffected individuals, 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.
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV000081908 SCV000920345 benign not specified 2017-09-18 criteria provided, single submitter clinical testing Variant summary: c.6530-4dupT in VPS13B gene is an intronic change that involves a non-conserved nucleotide. 5/5 programs in Alamut predict that this variant does not affect a normal splicing, however no functional studies supporting this notion were published at the time of evaluation. The variant is present in the control population dataset of ExAC at frequency of 0.01956 (1930/98690 chrs tested, including 49 homozygotes), predominantly in individuals of South Asian descent (0.068; 1002/14612 chrs tested). The observed frequency greatly exceeds the maximum expected allele frequency for a pathogenic variant of 0.0025, suggesting that it is likely to be a common polymorphism. The variant of interest has not, to our knowledge, been reported in affected individuals in published reports but is cited as Likely Benign/Benign by reputable database/clinical laboratory. Taking together, the variant was classified as Benign.
Invitae RCV000371009 SCV001724455 benign Cohen syndrome 2024-02-01 criteria provided, single submitter clinical testing
GeneDx RCV001650927 SCV001870204 benign not provided 2020-07-24 criteria provided, single submitter clinical testing

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