Submissions for variant NM_001199397.3(NEK1):c.1388C>T (p.Ala463Val)

gnomAD frequency: 0.03694  dbSNP: rs34540355

Total submissions: 8

Submitter	RCV	SCV	Clinical significance	Condition	Last evaluated	Review status	Method	Comment
Illumina Laboratory Services, Illumina	RCV000540144	SCV000448565	benign	Short-rib thoracic dysplasia 6 with or without polydactyly	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	RCV000428150	SCV000516281	benign	not specified	2016-04-26	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.
Invitae	RCV000540144	SCV000627781	benign	Short-rib thoracic dysplasia 6 with or without polydactyly	2024-01-31	criteria provided, single submitter	clinical testing
Genome Diagnostics Laboratory, University Medical Center Utrecht	RCV000540144	SCV000743657	likely benign	Short-rib thoracic dysplasia 6 with or without polydactyly	2016-05-13	criteria provided, single submitter	clinical testing
Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center	RCV000540144	SCV000744994	benign	Short-rib thoracic dysplasia 6 with or without polydactyly	2015-09-21	criteria provided, single submitter	clinical testing
Genome Diagnostics Laboratory, The Hospital for Sick Children	RCV002278576	SCV002566926	benign	Connective tissue disorder	2022-05-17	criteria provided, single submitter	clinical testing
Laboratory of Diagnostic Genome Analysis, Leiden University Medical Center (LUMC)	RCV001573270	SCV001798870	likely benign	not provided		no assertion criteria provided	clinical testing
Clinical Genetics, Academic Medical Center	RCV000428150	SCV001923497	benign	not specified		no assertion criteria provided	clinical testing