ClinVar Miner

Submissions for variant NM_001384732.1(CPLANE1):c.1809T>C (p.Thr603=)

gnomAD frequency: 0.01890  dbSNP: rs115435816
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Total submissions: 8
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
PreventionGenetics, part of Exact Sciences RCV000145356 SCV000314177 benign not specified criteria provided, single submitter clinical testing
Illumina Laboratory Services, Illumina RCV000368176 SCV000457414 benign Joubert syndrome 17 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 benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease.
GeneDx RCV000145356 SCV000516888 benign not specified 2016-09-12 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 RCV000543556 SCV000647806 benign not provided 2024-01-30 criteria provided, single submitter clinical testing
Fulgent Genetics, Fulgent Genetics RCV002505124 SCV002805383 benign Orofaciodigital syndrome type 6; Joubert syndrome 17 2021-09-01 criteria provided, single submitter clinical testing
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV000145356 SCV004241407 benign not specified 2023-12-13 criteria provided, single submitter clinical testing Variant summary: CPLANE1 c.1809T>C results in a synonymous change. The variant allele was found at a frequency of 0.0032 in 1543388 control chromosomes in the gnomAD database, including 147 homozygotes. The observed variant frequency is approximately 2.17 fold of the estimated maximal expected allele frequency for a pathogenic variant in CPLANE1 causing Joubert Syndrome And Related Disorders phenotype (0.0015), strongly suggesting that the variant is benign. Four submitters have cited clinical-significance assessments for this variant to ClinVar after 2014. All submitters classified the variant as benign. Based on the evidence outlined above, the variant was classified as benign.
Breakthrough Genomics, Breakthrough Genomics RCV000543556 SCV005305102 benign not provided criteria provided, single submitter not provided
Genetic Services Laboratory, University of Chicago RCV000145356 SCV000192435 likely benign not specified no assertion criteria provided clinical testing

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