ClinVar Miner

Submissions for variant NM_014956.5(CEP164):c.3610-4A>G

gnomAD frequency: 0.00025  dbSNP: rs111915712
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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Labcorp Genetics (formerly Invitae), Labcorp RCV001439470 SCV001642356 likely benign Nephronophthisis 15 2024-12-02 criteria provided, single submitter clinical testing
Fulgent Genetics, Fulgent Genetics RCV001439470 SCV002803394 likely benign Nephronophthisis 15 2021-11-11 criteria provided, single submitter clinical testing
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV005056662 SCV005727038 uncertain significance not specified 2024-11-06 criteria provided, single submitter clinical testing Variant summary: CEP164 c.3610-4A>G alters a nucleotide located close to a canonical splice site and therefore could affect mRNA splicing, leading to a significantly altered protein sequence. Consensus agreement among computation tools predict no significant impact on normal splicing. However, these predictions have yet to be confirmed by functional studies. The variant allele was found at a frequency of 7.2e-05 in 1614066 control chromosomes, predominantly at a frequency of 0.0011 within the African or African-American subpopulation in the gnomAD database, including 1 homozygotes. This frequency is not significantly higher than estimated for a pathogenic variant in CEP164 causing Nephronophthisis 15, allowing no conclusion about variant significance. To our knowledge, no occurrence of c.3610-4A>G in individuals affected with Nephronophthisis 15 and no experimental evidence demonstrating its impact on protein function have been reported. ClinVar contains an entry for this variant (Variation ID: 720078). Based on the evidence outlined above, the variant was classified as VUS-possibly benign.
PreventionGenetics, part of Exact Sciences RCV003957994 SCV004782744 likely benign CEP164-related disorder 2021-07-09 no assertion criteria provided clinical testing This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications).

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