ClinVar Miner

Submissions for variant NM_012233.3(RAB3GAP1):c.1992G>A (p.Ser664=)

gnomAD frequency: 0.02952  dbSNP: rs7595725
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Total submissions: 6
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Illumina Laboratory Services, Illumina RCV000361670 SCV000416398 benign Warburg micro syndrome 1 2018-01-13 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 benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease.
GeneDx RCV000118092 SCV000522532 benign not specified 2016-05-06 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.
Labcorp Genetics (formerly Invitae), Labcorp RCV000878117 SCV001020971 benign not provided 2024-01-23 criteria provided, single submitter clinical testing
Breakthrough Genomics, Breakthrough Genomics RCV000878117 SCV005245279 benign not provided criteria provided, single submitter not provided
Genetic Services Laboratory, University of Chicago RCV000118092 SCV000152424 likely benign not specified no assertion criteria provided clinical testing Likely benign based on allele frequency in 1000 Genomes Project or ESP global frequency and its presence in a patient with a rare or unrelated disease phenotype. NOT Sanger confirmed.
PreventionGenetics, part of Exact Sciences RCV004529979 SCV004736566 benign RAB3GAP1-related disorder 2019-05-08 no assertion criteria provided clinical testing This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications).

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