ClinVar Miner

Submissions for variant NM_017890.4(VPS13B):c.2643A>T (p.Lys881Asn) (rs148777544)

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Total submissions: 6
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
EGL Genetic Diagnostics,Eurofins Clinical Diagnostics RCV000276527 SCV000342231 benign not specified 2016-06-21 criteria provided, single submitter clinical testing
Illumina Clinical Services Laboratory,Illumina RCV000358657 SCV000470779 likely benign Cohen syndrome 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 likely benign is not then subjected to further curation. The score for this variant resulted in a classification of likely benign for this disease.
Genetic Services Laboratory, University of Chicago RCV000276527 SCV000597915 uncertain significance not specified 2016-04-25 criteria provided, single submitter clinical testing
Invitae RCV000358657 SCV000755415 likely benign Cohen syndrome 2019-12-31 criteria provided, single submitter clinical testing
Ambry Genetics RCV000717328 SCV000848178 benign History of neurodevelopmental disorder 2018-02-07 criteria provided, single submitter clinical testing Insufficient evidence;General population or sub-population frequency is too high to be a pathogenic mutation based on disease/syndrome prevalence and penetrance
Center for Genomics, Ann and Robert H. Lurie Children's Hospital of Chicago RCV000358657 SCV001190480 uncertain significance Cohen syndrome 2019-03-25 criteria provided, single submitter clinical testing VPS13B NM_017890.4 exon 18 p.Lys881Asn (c.2643A>T): This variant has not been reported in the literature but is present in 0.8% (202/24970) of African alleles, including 1 homozygote in the Genome Aggregation Database (https://gnomad.broadinstitute.org/variant/8-100286553-A-T). This variant is present in ClinVar (Variation ID:288192). Evolutionary conservation suggests that this variant may impact the protein; computational predictive tools for this variant are unclear. In summary, data on this variant is insufficient for disease classification. Therefore, the clinical significance of this variant is uncertain.

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