ClinVar Miner

Submissions for variant NM_152564.5(VPS13B):c.6416A>G (p.Asn2139Ser)

gnomAD frequency: 0.00070  dbSNP: rs142248228
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Total submissions: 15
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Eurofins Ntd Llc (ga) RCV000711300 SCV000229838 uncertain significance not provided 2015-03-11 criteria provided, single submitter clinical testing
Genetic Services Laboratory, University of Chicago RCV000194104 SCV000249415 uncertain significance not specified 2015-04-02 criteria provided, single submitter clinical testing
Fulgent Genetics, Fulgent Genetics RCV000515269 SCV000611531 uncertain significance Cohen syndrome 2017-05-23 criteria provided, single submitter clinical testing
Invitae RCV000515269 SCV000755395 likely benign Cohen syndrome 2024-01-31 criteria provided, single submitter clinical testing
Athena Diagnostics RCV000711300 SCV000841640 uncertain significance not provided 2018-05-15 criteria provided, single submitter clinical testing
Ambry Genetics RCV002314637 SCV000849176 likely benign Inborn genetic diseases 2021-11-03 criteria provided, single submitter clinical testing This alteration is classified as likely 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 RCV000515269 SCV001190426 uncertain significance Cohen syndrome 2021-03-30 criteria provided, single submitter clinical testing VPS13B NM_017890.4 exon39 p.Asn2164Ser (c.6491A>G): This variant has not been reported in the literature but is present in 0.1% (48/30532) of South Asian alleles in the Genome Aggregation Database (https://gnomad.broadinstitute.org/variant/8-100712122-A-G). This variant is also present in ClinVar (Variation ID: 196985). This variant amino acid Serine (Ser) is present in 40 species including multiple mammals, and it is not well conserved among evolutionarily distant species; this suggests that this variant may not impact the protein. Additional computational prediction tools do not suggest an impact. In summary, data on this variant is insufficient for disease classification. Therefore, the clinical significance of this variant is uncertain.
Illumina Laboratory Services, Illumina RCV000515269 SCV001326106 uncertain significance Cohen syndrome 2018-03-02 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, this variant could not be ruled out of causing disease and therefore its association with disease required further investigation. A literature search was performed for the gene, cDNA change, and amino acid change (if applicable). No publications were found based on this search. This variant was therefore classified as a variant of unknown significance for this disease.
Genome-Nilou Lab RCV000515269 SCV001653495 uncertain significance Cohen syndrome 2021-05-18 criteria provided, single submitter clinical testing
GeneDx RCV000711300 SCV001823468 likely benign not provided 2020-07-29 criteria provided, single submitter clinical testing
New York Genome Center RCV000515269 SCV004046485 uncertain significance Cohen syndrome 2023-01-13 criteria provided, single submitter clinical testing
Institute of Human Genetics, University Hospital of Duesseldorf RCV000515269 SCV004046667 uncertain significance Cohen syndrome criteria provided, single submitter not provided
PreventionGenetics, part of Exact Sciences RCV003982929 SCV004797038 likely benign VPS13B-related disorder 2022-02-01 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).
CeGaT Center for Human Genetics Tuebingen RCV000711300 SCV004811028 likely benign not provided 2024-04-01 criteria provided, single submitter clinical testing VPS13B: BP4
Natera, Inc. RCV000515269 SCV001460395 likely benign Cohen syndrome 2020-01-02 no assertion criteria provided clinical testing

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