rs387906434
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Variant summary
Our verdict is Pathogenic. Variant got 18 ACMG points: 18P and 0B. PVS1PM2PP5_Very_Strong
The ENST00000360256.9(F8):βc.209_212delβ(p.Phe70Ter) variant causes a frameshift change. The variant allele was found at a frequency of 0.000000913 in 1,095,552 control chromosomes in the GnomAD database, with no homozygous occurrence. There are no hemizygote samples in GnomAD. Variant has been reported in ClinVar as Pathogenic (β β ). Variant results in nonsense mediated mRNA decay.
Frequency
Genomes: not found (cov: 22)
Exomes π: 9.1e-7 ( 0 hom. 0 hem. )
Consequence
F8
ENST00000360256.9 frameshift
ENST00000360256.9 frameshift
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 4.57
Genes affected
F8 (HGNC:3546): (coagulation factor VIII) This gene encodes coagulation factor VIII, which participates in the intrinsic pathway of blood coagulation; factor VIII is a cofactor for factor IXa which, in the presence of Ca+2 and phospholipids, converts factor X to the activated form Xa. This gene produces two alternatively spliced transcripts. Transcript variant 1 encodes a large glycoprotein, isoform a, which circulates in plasma and associates with von Willebrand factor in a noncovalent complex. This protein undergoes multiple cleavage events. Transcript variant 2 encodes a putative small protein, isoform b, which consists primarily of the phospholipid binding domain of factor VIIIc. This binding domain is essential for coagulant activity. Defects in this gene results in hemophilia A, a common recessive X-linked coagulation disorder. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Pathogenic. Variant got 18 ACMG points.
PVS1
Loss of function variant, product undergoes nonsense mediated mRNA decay. LoF is a known mechanism of disease.
PM2
Very rare variant in population databases, with high coverage;
PP5
Variant X-154999531-TACAA-T is Pathogenic according to our data. Variant chrX-154999531-TACAA-T is described in ClinVar as [Pathogenic]. Clinvar id is 10159.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chrX-154999531-TACAA-T is described in Lovd as [Likely_pathogenic].
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
F8 | NM_000132.4 | c.209_212del | p.Phe70Ter | frameshift_variant | 2/26 | ENST00000360256.9 | NP_000123.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
F8 | ENST00000360256.9 | c.209_212del | p.Phe70Ter | frameshift_variant | 2/26 | 1 | NM_000132.4 | ENSP00000353393 | P1 | |
F8 | ENST00000423959.5 | c.104_107del | p.Phe35Ter | frameshift_variant | 2/6 | 3 | ENSP00000409446 | |||
F8 | ENST00000453950.1 | c.191_194del | p.Phe64Ter | frameshift_variant | 3/5 | 3 | ENSP00000389153 | |||
F8 | ENST00000647125.1 | c.187_190del | p.Leu63ArgfsTer11 | frameshift_variant, stop_lost, NMD_transcript_variant | 2/14 | ENSP00000496062 |
Frequencies
GnomAD3 genomes Cov.: 22
GnomAD3 genomes
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22
GnomAD4 exome AF: 9.13e-7 AC: 1AN: 1095552Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 361164
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GnomAD4 genome Cov.: 22
GnomAD4 genome
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22
ClinVar
Significance: Pathogenic
Submissions summary: Pathogenic:5
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
Hereditary factor VIII deficiency disease Pathogenic:4
Pathogenic, criteria provided, single submitter | clinical testing | ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories | Jan 14, 2021 | The F8 c.209_212delTTGT; p.Phe70Ter variant (rs387906434), also known as c.208_211delTTTG, is published in the medical literature in numerous individuals with severe hemophilia A (Becker 1996, Habart 2003, Liu 1998, F8 database and references therein). Samples from affected individuals with this variant typically exhibit less than 1% of wildtype clotting activity (Habart 2003, Liu 1998, F8 database and references therein). This variant is absent from general population databases (Exome Variant Server, Genome Aggregation Database), indicating it is not a common polymorphism. This variant deletes 4 nucleotides, leads to an immediate stop codon and is predicted to result in a truncated protein or mRNA subject to non-sense mediated decay. Considering available information, this variant is considered to be pathogenic. References: Link to F8 database: http://www.factorviii-db.org Becker J et al. Characterization of the factor VIII defect in 147 patients with sporadic hemophilia A: family studies indicate a mutation type-dependent sex ratio of mutation frequencies. Am J Hum Genet. 1996 Apr;58(4):657-70. - |
Pathogenic, criteria provided, single submitter | clinical testing | Neuberg Centre For Genomic Medicine, NCGM | - | The F8 c.209_212del (p.Phe70Ter) variant has been reported in hemizygous state in individuals affected with Hemophilia A (Habart 2003). This variant has been reported to the ClinVar database as Pathogenic. The p.Phe70Ter variant is novel (not in any individuals) in gnomAD Exomes and is novel (not in any individuals) in 1000 Genomes. This variant is predicted to cause loss of normal protein function through protein truncation. Loss of function variants have been previously reported to be disease causing. For these reasons, this variant has been classified as Pathogenic. - |
Pathogenic, criteria provided, single submitter | clinical testing | Genetics and Molecular Pathology, SA Pathology | May 05, 2021 | - - |
Pathogenic, no assertion criteria provided | literature only | OMIM | Jan 01, 1995 | - - |
not provided Pathogenic:1
Pathogenic, criteria provided, single submitter | clinical testing | Mayo Clinic Laboratories, Mayo Clinic | Apr 16, 2024 | PM2_moderate, PM6, PS4_moderate, PVS1 - |
Computational scores
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at