ClinVar Miner

Submissions for variant NM_000133.4(F9):c.839-1G>A

dbSNP: rs1439169192
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories RCV001812588 SCV002049751 pathogenic not provided 2021-07-01 criteria provided, single submitter clinical testing The F9 c.839-1G>A variant (rs1439169192) is reported in the literature in multiple individuals affected with severe hemophilia B (see factor VI and references therein). This variant is absent from the Genome Aggregation Database, indicating it is not a common polymorphism. This variant disrupts the canonical splice acceptor site of intron seven, which is likely to negatively impact gene function. Based on available information, this variant is considered to be pathogenic References: Link to Factor VI database: https://f9-db.eahad.org/index.php
Labcorp Genetics (formerly Invitae), Labcorp RCV003772215 SCV004571523 pathogenic Hereditary factor IX deficiency disease; Thrombophilia, X-linked, due to factor 9 defect 2024-01-15 criteria provided, single submitter clinical testing This sequence change affects an acceptor splice site in intron 7 of the F9 gene. While this variant is not anticipated to result in nonsense mediated decay, it likely alters RNA splicing and results in a disrupted protein product. This variant is not present in population databases (gnomAD no frequency). Disruption of this splice site has been observed in individuals with Hemophilia B (PMID: 2020563, 2212858, 30817051; Invitae). ClinVar contains an entry for this variant (Variation ID: 1331043). 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 disrupt the consensus splice site. For these reasons, this variant has been classified as Pathogenic.
OMIM RCV001815042 SCV000031563 pathogenic Hereditary factor IX deficiency disease 2013-09-11 no assertion criteria provided literature only

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