rs5990
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_001994.3(F13B):c.1953-56T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.493 in 1,410,192 control chromosomes in the GnomAD database, including 179,483 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.44 ( 16594 hom., cov: 32)
Exomes 𝑓: 0.50 ( 162889 hom. )
Consequence
F13B
NM_001994.3 intron
NM_001994.3 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.503
Genes affected
F13B (HGNC:3534): (coagulation factor XIII B chain) This gene encodes coagulation factor XIII B subunit. Coagulation factor XIII is the last zymogen to become activated in the blood coagulation cascade. Plasma factor XIII is a heterotetramer composed of 2 A subunits and 2 B subunits. The A subunits have catalytic function, and the B subunits do not have enzymatic activity and may serve as a plasma carrier molecules. Platelet factor XIII is comprised only of 2 A subunits, which are identical to those of plasma origin. Upon activation by the cleavage of the activation peptide by thrombin and in the presence of calcium ion, the plasma factor XIII dissociates its B subunits and yields the same active enzyme, factor XIIIa, as platelet factor XIII. This enzyme acts as a transglutaminase to catalyze the formation of gamma-glutamyl-epsilon-lysine crosslinking between fibrin molecules, thus stabilizing the fibrin clot. Factor XIII deficiency is classified into two categories: type I deficiency, characterized by the lack of both the A and B subunits; and type II deficiency, characterized by the lack of the A subunit alone. These defects can result in a lifelong bleeding tendency, defective wound healing, and habitual abortion. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -14 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.88).
BP6
?
Variant 1-197039467-A-C is Benign according to our data. Variant chr1-197039467-A-C is described in ClinVar as [Benign]. Clinvar id is 1270193.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.8 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
F13B | NM_001994.3 | c.1953-56T>G | intron_variant | ENST00000367412.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
F13B | ENST00000367412.2 | c.1953-56T>G | intron_variant | 1 | NM_001994.3 | P1 | |||
F13B | ENST00000649282.1 | c.708-56T>G | intron_variant |
Frequencies
GnomAD3 genomes ? AF: 0.442 AC: 67095AN: 151716Hom.: 16582 Cov.: 32
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GnomAD4 exome AF: 0.499 AC: 628409AN: 1258356Hom.: 162889 AF XY: 0.502 AC XY: 319046AN XY: 635786
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GnomAD4 genome ? AF: 0.442 AC: 67128AN: 151836Hom.: 16594 Cov.: 32 AF XY: 0.452 AC XY: 33545AN XY: 74168
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jun 18, 2021 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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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