ClinVar Genomic variation as it relates to human health

The variant is observed at an extremely low frequency in the gnomAD v2.1.1 dataset (total allele frequency: 0.001%). In silico tools predict the variant to alter splicing and produce an abnormal transcript (SpliceAI: 0.83). The variant has been reported at least twice as pathogenic (ClinVar ID: VCV000439678 / PMID: 1301932, 15670040, 16972227, 1923751) and observed in multiple (>3) similarly affected unrelated individuals (PMID: 1301932, 15670040, 16972227, 1923751). Therefore, this variant is classified as Pathogenic according to the recommendation of ACMG/AMP guideline.

PP3, PP5, PM2, PM3, PS2, PS4_moderate

The F8 c.1569G>T; p.Leu523= variant (rs782733685), also known as Leu504=, is described in the medical literature in several individuals with mild hemophilia (Bogdanova 2007, Diamond 1992, El-Maarri 2005, Green 2008, Tavassoli 1998, Tuddenham 1991, Vidal 2001). This variant is reported in ClinVar (Variation ID: 439678), and is only observed on two alleles in the Genome Aggregation Database, indicating it is not a common polymorphism. This is a synonymous variant in a weakly conserved nucleotide, but computational analyses (Alamut v.2.11) predict that this variant may impact splicing by creating a novel cryptic acceptor splice site. Functional studies show that this variant results in altered mRNA splicing that deletes 36 nucleotides from exon 11, leaving the rest of the protein in frame (El-Maarri 2005, Tavassoli 1998). Based on available information, the p.Leu523= variant is considered to be pathogenic. References: Bogdanova N et al. Spectrum of molecular defects and mutation detection rate in patients with mild and moderate hemophilia A. Hum Mutat. 2007 Jan;28(1):54-60. PMID: 16972227. Diamond C et al. Amino acid substitutions in conserved domains of factor VIII and related proteins: study of patients with mild and moderately severe hemophilia A. Hum Mutat. 1992 1(3):248-57. PMID: 1301932. El-Maarri O et al. Analysis of mRNA in hemophilia A patients with undetectable mutations reveals normal splicing in the factor VIII gene. J Thromb Haemost. 2005 Feb;3(2):332-9. PMID: 15670040. Green PM et al. Haemophilia A mutations in the UK: results of screening one-third of the population. Br J Haematol. 2008 Oct;143(1):115-28. PMID: 18691168. Tavassoli K et al. Identification of four novel mutations in the factor VIII gene: three missense mutations (E1875G, G2088S, I2185T) and a 2-bp deletion (1780delTC). Hum Mutat. 1998 Suppl 1:S260-2. PMID: 9792405. Tuddenham EG et al. Haemophilia A: database of nucleotide substitutions, deletions, insertions and rearrangements of the factor VIII gene. Nucleic Acids Res. 1991 19(18):4821-33. PMID: 1923751. Vidal F et al. Rapid hemophilia A molecular diagnosis by a simple DNA sequencing procedure: identification of 14 novel mutations. Thromb Haemost. 2001 Apr;85(4):580-3. PMID: 11341489.

Observed in hemizygous state in multiple unrelated patients with hemophilia in published literature and tested at GeneDx, and not observed in hemizygous state in controls (PMID: 1639429, 11341489, 16972227, 20331761, 31877800, 30690819); Published functional studies demonstrate a damaging effect on splicing (PMID: 9792405, 30690819); In silico analysis supports a deleterious effect on splicing; This variant is associated with the following publications: (PMID: 15670040, 33314404, 30690819, 9792405, 1301932, 18387975, 35770352, 11341489, 16972227, 18691168, 29296726, 28488976, 23088352, 33805278, 20331761, 27824209, 31877800, 1639429)

Variant summary: F8 c.1569G>T alters a non-conserved nucleotide resulting in a synonymous change. Computational tools predict a significant impact on normal splicing: Two predict the variant strengthens a cryptic 3' acceptor site. One predict the variant no significant impact on splicing. At least one publication reports experimental evidence that this variant affects mRNA splicing (Tavassoli_1998). The variant allele was found at a frequency of 1.1e-05 in 183163 control chromosomes (gnomAD). c.1569G>T has been reported in the literature in multiple individuals affected with Factor VIII Deficiency (Hemophilia A; e.g. Economou_1992, Tavassoli_1998, Miller_2012). These data indicate that the variant is very likely to be associated with disease. The following publications have been ascertained in the context of this evaluation (PMID: 1639429, 9792405, 22103590). ClinVar contains an entry for this variant (Variation ID: 439678). Based on the evidence outlined above, the variant was classified as pathogenic.