ClinVar Miner

Submissions for variant NM_000350.3(ABCA4):c.3050+5G>A

gnomAD frequency: 0.00002  dbSNP: rs61751262
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Total submissions: 5
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000085541 SCV000616626 pathogenic not provided 2024-04-15 criteria provided, single submitter clinical testing RNA studies demonstrate that c.3050+5G>A destroys the natural donor site for intron 20, causing skipping of exon 20 (PMID: 29162642); In silico analysis supports a deleterious effect on splicing; This variant is associated with the following publications: (PMID: 35120629, 35775617, 31964843, 35076026, 19217903, 25301883, 20647261, 25525159, 11726554, 26024099, 28044389, 22076985, 35119454, 32619608, 31456290, 30055151, 10958763, 37217489, 29162642)
Labcorp Genetics (formerly Invitae), Labcorp RCV000085541 SCV001201300 pathogenic not provided 2024-01-04 criteria provided, single submitter clinical testing This sequence change falls in intron 20 of the ABCA4 gene. It does not directly change the encoded amino acid sequence of the ABCA4 protein. RNA analysis indicates that this variant induces altered splicing and likely results in a shortened protein product. This variant is present in population databases (rs61751262, gnomAD 0.03%). This variant has been observed in individual(s) with Stargardt disease (PMID: 10958763, 11726554, 19217903). In at least one individual the data is consistent with being in trans (on the opposite chromosome) from a pathogenic variant. This variant is also known as IVS20+5G>A. ClinVar contains an entry for this variant (Variation ID: 99192). Variants that disrupt the consensus splice site are a relatively common cause of aberrant splicing (PMID: 17576681, 9536098). Studies have shown that this variant results in skipping of exon 20, but is expected to preserve the integrity of the reading-frame (PMID: 29162642). For these reasons, this variant has been classified as Pathogenic.
Blueprint Genetics RCV001073618 SCV001239169 pathogenic Retinal dystrophy 2019-07-19 criteria provided, single submitter clinical testing
Retina International RCV000085541 SCV000117678 not provided not provided no assertion provided not provided
Sharon lab, Hadassah-Hebrew University Medical Center RCV001002836 SCV001160855 pathogenic Stargardt disease 2019-06-23 no assertion criteria provided research

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