ClinVar Miner

Submissions for variant NM_017890.4(VPS13B):c.7783G>A (p.Asp2595Asn) (rs140179844)

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Total submissions: 7
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
EGL Genetic Diagnostics,Eurofins Clinical Diagnostics RCV000723691 SCV000113850 uncertain significance not provided 2013-08-28 criteria provided, single submitter clinical testing
GeneDx RCV000081915 SCV000491577 uncertain significance not specified 2016-09-26 criteria provided, single submitter clinical testing The D2595N variant has not been published as a pathogenic variant, nor has it been reported as a benign variant to our knowledge. The NHLBI Exome Sequencing Project reports D2595N was observed in 16 of 4406 (0.36%) alleles from individuals of African American background, and the 1000 Genomes Project Consortium reports it was observed in 5 of 198 (2.53%) alleles in an African sub-population. The D2595N variant is a semi-conservative amino acid substitution, which may impact secondary protein structure as these residues differ in some properties. This substitution occurs at a position that is conserved in mammals and in silico analysis predicts this variant is probably damaging to the protein structure/function. Therefore, based on the currently available information, it is unclear whether this variant is pathogenic or a rare benign variant.
Invitae RCV000634120 SCV000755406 likely benign Cohen syndrome 2019-12-31 criteria provided, single submitter clinical testing
Counsyl RCV000634120 SCV000796759 uncertain significance Cohen syndrome 2017-12-28 criteria provided, single submitter clinical testing
Ambry Genetics RCV000717710 SCV000848568 likely benign History of neurodevelopmental disorder 2018-08-24 criteria provided, single submitter clinical testing In silico models in agreement (benign) ;Sub-population frequency in support of benign classification (not ava blue, manual h-w)
Illumina Clinical Services Laboratory,Illumina RCV000634120 SCV001324018 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.
Biochemical Molecular Genetic Laboratory,King Abdulaziz Medical City RCV000634120 SCV001133239 likely pathogenic Cohen syndrome 2019-09-26 no assertion criteria provided clinical testing

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