ClinVar Miner

Submissions for variant NM_025114.4(CEP290):c.1623+2C>A

gnomAD frequency: 0.00001  dbSNP: rs2039218006
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Labcorp Genetics (formerly Invitae), Labcorp RCV001941065 SCV002217226 uncertain significance Familial aplasia of the vermis; Meckel-Gruber syndrome; Nephronophthisis 2023-08-10 criteria provided, single submitter clinical testing In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. Variants that disrupt the consensus splice site are a relatively common cause of aberrant splicing (PMID: 17576681, 9536098). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. This sequence change falls in intron 16 of the CEP290 gene. It does not directly change the encoded amino acid sequence of the CEP290 protein. It affects a nucleotide within the consensus splice site. This variant is not present in population databases (gnomAD no frequency). This variant has been observed in individual(s) with autosomal recessive Leber congenital amaurosis (PMID: 32865313). ClinVar contains an entry for this variant (Variation ID: 1432036).
Fulgent Genetics, Fulgent Genetics RCV002484634 SCV002799669 uncertain significance Leber congenital amaurosis 10; Meckel syndrome, type 4; Senior-Loken syndrome 6; Joubert syndrome 5; Bardet-Biedl syndrome 14 2022-04-01 criteria provided, single submitter clinical testing
PreventionGenetics, part of Exact Sciences RCV004733422 SCV005355322 likely pathogenic CEP290-related disorder 2024-01-04 no assertion criteria provided clinical testing The CEP290 c.1623+2C>A variant is predicted to interfere with splicing. This variant was reported in an individual with retinal dystrophy (Sallum et al. 2020. PubMed ID: 32865313). This variant has not been reported in a large population database (http://gnomad.broadinstitute.org), indicating this variant is rare. Variants that disrupt the consensus splice donor site in CEP290 are expected to be pathogenic. This variant is interpreted as likely pathogenic.

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