ClinVar Miner

Submissions for variant NM_001365999.1(SZT2):c.9286+5G>A

gnomAD frequency: 0.00015  dbSNP: rs367775055
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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000485962 SCV000565609 uncertain significance not provided 2021-07-12 criteria provided, single submitter clinical testing In silico analysis supports a deleterious effect on splicing; Has not been previously published as pathogenic or benign to our knowledge; This variant is associated with the following publications: (PMID: 27535533)
Invitae RCV000485962 SCV000943374 uncertain significance not provided 2022-09-27 criteria provided, single submitter clinical testing This sequence change falls in intron 65 of the SZT2 gene. It does not directly change the encoded amino acid sequence of the SZT2 protein. It affects a nucleotide within the consensus splice site. This variant is present in population databases (rs367775055, gnomAD 0.02%). This variant has not been reported in the literature in individuals affected with SZT2-related conditions. ClinVar contains an entry for this variant (Variation ID: 418511). 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 create or strengthen a splice site. 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.
CeGaT Center for Human Genetics Tuebingen RCV000485962 SCV002496873 likely benign not provided 2022-07-01 criteria provided, single submitter clinical testing SZT2: BP4
Ambry Genetics RCV002374883 SCV002684202 uncertain significance Inborn genetic diseases 2018-01-24 criteria provided, single submitter clinical testing The c.9115+5G>A intronic variant results from a G to A substitution 5 nucleotides after coding exon 65 in the SZT2 gene. This nucleotide position is well conserved in available vertebrate species. Using two different splice site prediction tools, this alteration is predicted by BDGP to abolish the native splice donor site, but is predicted to weaken (but not abolish) the efficiency of the native splice donor site by ESEfinder; however, direct evidence is unavailable. Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear.

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