ClinVar Miner

Submissions for variant NM_152564.5(VPS13B):c.2643A>T (p.Lys881Asn)

gnomAD frequency: 0.00243  dbSNP: rs148777544
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Total submissions: 8
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Eurofins Ntd Llc (ga) RCV000276527 SCV000342231 benign not specified 2016-06-21 criteria provided, single submitter clinical testing
Illumina Laboratory Services, 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 2024-01-31 criteria provided, single submitter clinical testing
Ambry Genetics RCV002314026 SCV000848178 benign Inborn genetic diseases 2018-02-07 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.
Center for Genomics, Ann and Robert H. Lurie Children's Hospital of Chicago RCV000358657 SCV001190480 uncertain significance Cohen syndrome 2021-03-30 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.
PreventionGenetics, part of Exact Sciences RCV003977797 SCV004798060 likely benign VPS13B-related disorder 2020-01-20 criteria provided, single submitter clinical testing This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications).
Natera, Inc. RCV000358657 SCV002079525 benign Cohen syndrome 2019-10-29 no assertion criteria provided clinical testing

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