ClinVar Miner

Submissions for variant NM_006949.4(STXBP2):c.1453-9G>A

gnomAD frequency: 0.00003  dbSNP: rs372742473
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Total submissions: 2
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Labcorp Genetics (formerly Invitae), Labcorp RCV000541503 SCV000648530 uncertain significance Familial hemophagocytic lymphohistiocytosis 5 2022-10-25 criteria provided, single submitter clinical testing This sequence change falls in intron 16 of the STXBP2 gene. It does not directly change the encoded amino acid sequence of the STXBP2 protein. This variant is present in population databases (rs372742473, gnomAD 0.006%). This variant has not been reported in the literature in individuals affected with STXBP2-related conditions. ClinVar contains an entry for this variant (Variation ID: 470699). 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.
Genetic Services Laboratory, University of Chicago RCV001821570 SCV002065191 uncertain significance not specified 2021-04-19 criteria provided, single submitter clinical testing DNA sequence analysis of the STXBP2 gene demonstrated a sequence change in intron 16, c.1453-9G>A. This change does not appear to have been previously described in individuals with STXBP2-related disorders. This sequence change has been described in the gnomAD database with a low frequency of 0.006% in Latino/Admixed American subpopulation (dbSNP rs372742473). This sequence change is predicted to have a deleterious effect on splicing based on in silico splice prediction programs. It is possible that this sequence change represents a benign sequence change in the STXBP2 gene that has not been identified to date. The functional significance of this sequence change is not known at present and its contribution to this patient's disease phenotype cannot definitively be determined.

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