Submissions for variant NM_000132.4(F8):c.5587-93C>T

dbSNP: rs1264918703

Total submissions: 6

Submitter	RCV	SCV	Clinical significance	Condition	Last evaluated	Review status	Method	Comment
Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine	RCV001195277	SCV001365586	likely pathogenic	Hereditary factor VIII deficiency disease	2019-08-09	criteria provided, single submitter	clinical testing	The c.5587-93C>T variant in F8 has been previously reported in 2 individuals with mild hemophilia A (Castaman 2011, Back 2015), but was absent from large population studies. This variant occurs outside of the splice consensus region in intron 16. However, both in silico prediction tools and in vitro functional assays suggest that the variant creates a novel splice donor site, leading to the insertion of 56bp of intronic sequence in the mRNA (Castaman 2011). This insertion, in turn, is predicted to cause a frameshift and the introduction of a premature termination codon within the inserted sequence, leading to a truncated or absent protein. Loss of function of the F8 gene is an established disease mechanism in X-linked hemophilia A. In summary, this variant meets criteria to be classified as likely pathogenic for X-linked hemophilia A, though it may be associated with a mild form of the disease. ACMG/AMP Criteria applied: PM2, PS3_moderate, PP4, PS4_Supporting.
GeneDx	RCV001552989	SCV001773780	pathogenic	not provided	2021-06-29	criteria provided, single submitter	clinical testing	Non-canonical splice site variant demonstrated to result in loss-of-function (Castaman G, 2011; Bach JE, 2016); No data available from control populations to assess the frequency of this variant; This variant is associated with the following publications: (PMID: 21689372, 29357978, 27824209, 26246214, 29652675, 25948085, 23809411)
CeGaT Center for Human Genetics Tuebingen	RCV001552989	SCV002546222	likely pathogenic	not provided	2022-04-01	criteria provided, single submitter	clinical testing	F8: PS3, PM2, PP3
Center for Genomic Medicine, Rigshospitalet, Copenhagen University Hospital	RCV001552989	SCV004024684	likely pathogenic	not provided	2023-08-15	criteria provided, single submitter	clinical testing
Women's Health and Genetics/Laboratory Corporation of America, LabCorp	RCV001195277	SCV004241393	likely pathogenic	Hereditary factor VIII deficiency disease	2023-12-21	criteria provided, single submitter	clinical testing	Variant summary: F8 c.5587-93C>T is located at a position not widely known to affect splicing. Consensus agreement among computation tools predict no significant impact on normal splicing. However, at least one publication reports experimental evidence that this variant affects mRNA splicing by introducing a 56 bp fragment of intron 16, that may lead to a frameshift resulting in a premature stop codon via mRNA analysis in HEK293 cells (Castaman_2011). The variant was absent in 21822 control chromosomes. c.5587-93C>T has been reported in the literature in at-least two individuals affected with mild Factor VIII Deficiency (Hemophilia A) (example, Castaman_2011, Bach_2015). These data indicate that the variant may be associated with disease. The following publications have been ascertained in the context of this evaluation (PMID: 25948085, 21689372). Four submitters have cited clinical-significance assessments for this variant to ClinVar after 2014. All submitters classified the variant as pathogenic/likely pathogenic. Based on the evidence outlined above, the variant was classified as likely pathogenic.
ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories	RCV001552989	SCV004562728	likely pathogenic	not provided	2023-04-07	criteria provided, single submitter	clinical testing	The F8 c.5587-93C>T variant (rs1264918703) is reported in the literature in individuals affected with mild hemophilia A (Bach 2015, Castaman 2011). This variant is also reported in ClinVar (Variation ID: 929936), but is absent from the Genome Aggregation Database, indicating it is not a common polymorphism. This is an intronic variant in a weakly conserved nucleotide, but computational analyses (Alamut Visual Plus v.1.5.1) predict that this variant may impact splicing by creating a novel cryptic donor splice site. Additionally, in vitro functional assays show inclusion of 56bp of intron 16 leading to a frameshift, so it is predicted to result in a truncated protein or mRNA subject to nonsense-mediated decay (Castaman 2011). Based on available information, this variant is considered to be likely pathogenic. References: Bach JE et al. Identification of deep intronic variants in 15 haemophilia A patients by next generation sequencing of the whole factor VIII gene. Thromb Haemost. 2015 Oct;114(4):757-67. PMID: 25948085. Castaman G et al. Deep intronic variations may cause mild hemophilia A. J Thromb Haemost. 2011 Aug;9(8):1541-8. PMID: 21689372.