ClinVar Miner

Submissions for variant NM_000501.4(ELN):c.164-2A>C

gnomAD frequency: 0.00004  dbSNP: rs782096458
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000430802 SCV000518342 uncertain significance not provided 2023-01-12 criteria provided, single submitter clinical testing Canonical splice site variant with an unclear effect on protein function; Has not been previously published as pathogenic or benign to our knowledge; This variant is associated with the following publications: (PMID: 31589614)
Invitae RCV001210534 SCV001382026 likely pathogenic Supravalvar aortic stenosis 2019-06-28 criteria provided, single submitter clinical testing In summary, the currently available evidence indicates that the variant is pathogenic, but additional data are needed to prove that conclusively. Therefore, this variant has been classified as Likely Pathogenic. Donor and acceptor splice site variants typically lead to a loss of protein function (PMID: 16199547), and loss-of-function variants in ELN are known to be pathogenic (PMID: 11175284). This variant has not been reported in the literature in individuals with ELN-related conditions. ClinVar contains an entry for this variant (Variation ID: 380361). This variant is present in population databases (rs782096458, ExAC 0.002%). This sequence change affects an acceptor splice site in intron 3 of the ELN gene. It is expected to disrupt RNA splicing and likely results in an absent or disrupted protein product.
PreventionGenetics, part of Exact Sciences RCV004539797 SCV004797212 likely pathogenic ELN-related disorder 2023-12-07 criteria provided, single submitter clinical testing The ELN c.164-2A>C variant is predicted to disrupt the AG splice acceptor site and interfere with normal splicing. To our knowledge, this variant has not been reported in a patient with an ELN related disorder. This variant is reported in 0.014% of alleles in individuals of Latino descent in gnomAD. Variants that disrupt the consensus splice acceptor site in ELN are expected to be pathogenic. This variant is interpreted as likely pathogenic.

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