ClinVar Miner

Submissions for variant NM_000350.3(ABCA4):c.5836-3C>A

gnomAD frequency: 0.00001  dbSNP: rs1064793013
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000483369 SCV000564538 likely pathogenic not provided 2013-07-31 criteria provided, single submitter clinical testing The c.5836-3 C>A variant in the ABCA4 gene has not been reported as a pathogenic mutation or as a benign polymorphism to our knowledge. Three in silico splice prediction algorithms predict c.5836-3 C>A destroys or damages the natural splice acceptor site of intron 41. The c.5836-3 C>A variant was not observed in approximately 6,500 individuals of European and African American ancestry in an external variant database, indicating it is not a common benign variant in these populations. Therefore, the c.5836-3C>A variant is a candidate for a pathogenic variant, although the possibility that it is a benign polymorphism cannot be completely excluded.
Labcorp Genetics (formerly Invitae), Labcorp RCV000483369 SCV003523329 uncertain significance not provided 2022-07-01 criteria provided, single submitter clinical testing This sequence change falls in intron 41 of the ABCA4 gene. It does not directly change the encoded amino acid sequence of the ABCA4 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 ABCA4-related conditions (PMID: 25082829). ClinVar contains an entry for this variant (Variation ID: 417993). Variants that disrupt the consensus splice site are a relatively common cause of aberrant splicing (PMID: 17576681, 9536098). Studies have shown that this variant is associated with altered splicing resulting in the insertion of 30 nucleotides into the transcript (PMID: 29162642, 32413971). 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.
Rui Chen Lab, Baylor College of Medicine RCV000515665 SCV000579423 pathogenic Retinitis pigmentosa 2017-05-09 no assertion criteria provided research

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