ClinVar Miner

Submissions for variant NM_001365999.1(SZT2):c.1091-1G>A

dbSNP: rs1652173183
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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 RCV001215323 SCV001387061 likely pathogenic not provided 2023-08-30 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. Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. ClinVar contains an entry for this variant (Variation ID: 944833). This variant has not been reported in the literature in individuals affected with SZT2-related conditions. This variant is not present in population databases (gnomAD no frequency). This sequence change affects an acceptor splice site in intron 8 of the SZT2 gene. It is expected to disrupt RNA splicing. Variants that disrupt the donor or acceptor splice site typically lead to a loss of protein function (PMID: 16199547), and loss-of-function variants in SZT2 are known to be pathogenic (PMID: 23932106, 27248490, 28556953).
GeneDx RCV001215323 SCV004012656 likely pathogenic not provided 2023-01-10 criteria provided, single submitter clinical testing Canonical splice site variant expected to result in aberrant splicing, although in the absence of functional evidence the actual effect of this sequence change is unknown.; Not observed at significant frequency in large population cohorts (gnomAD); Has not been previously published as pathogenic or benign to our knowledge
Genome-Nilou Lab RCV003446657 SCV004174038 likely pathogenic Developmental and epileptic encephalopathy, 18 2023-04-11 criteria provided, single submitter clinical testing

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