ClinVar Miner

Submissions for variant NM_001199397.3(NEK1):c.2764+12T>A

gnomAD frequency: 0.01594  dbSNP: rs77658514
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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Illumina Laboratory Services, Illumina RCV000314339 SCV000448551 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 RCV000420702 SCV000516509 benign not specified 2017-01-03 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.
ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories RCV001812883 SCV001158804 benign not provided 2023-11-03 criteria provided, single submitter clinical testing
Invitae RCV000314339 SCV002407526 benign Short-rib thoracic dysplasia 6 with or without polydactyly 2024-01-29 criteria provided, single submitter clinical testing

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