rs5986
Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1
The NM_000129.4(F13A1):c.1704A>G(p.Glu568=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0861 in 1,614,104 control chromosomes in the GnomAD database, including 6,513 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Genomes: 𝑓 0.076 ( 502 hom., cov: 32)
Exomes 𝑓: 0.087 ( 6011 hom. )
Consequence
F13A1
NM_000129.4 synonymous
NM_000129.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.234
Genes affected
F13A1 (HGNC:3531): (coagulation factor XIII A chain) This gene encodes the coagulation factor XIII A 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 plasma carrier molecules. Platelet factor XIII is comprised only of 2 A subunits, which are identical to those of plasma origin. Upon 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. It also crosslinks alpha-2-plasmin inhibitor, or fibronectin, to the alpha chains of fibrin. 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 -21 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.55).
BP6
?
Variant 6-6174623-T-C is Benign according to our data. Variant chr6-6174623-T-C is described in ClinVar as [Likely_benign]. Clinvar id is 255184.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr6-6174623-T-C is described in Lovd as [Benign].
BP7
?
Synonymous conserved (PhyloP=0.234 with no splicing effect.
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0936 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
F13A1 | NM_000129.4 | c.1704A>G | p.Glu568= | synonymous_variant | 12/15 | ENST00000264870.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
F13A1 | ENST00000264870.8 | c.1704A>G | p.Glu568= | synonymous_variant | 12/15 | 1 | NM_000129.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0758 AC: 11527AN: 152132Hom.: 502 Cov.: 32
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GnomAD3 exomes AF: 0.0721 AC: 18137AN: 251432Hom.: 805 AF XY: 0.0738 AC XY: 10024AN XY: 135880
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GnomAD4 exome AF: 0.0872 AC: 127404AN: 1461854Hom.: 6011 Cov.: 40 AF XY: 0.0866 AC XY: 62966AN XY: 727232
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GnomAD4 genome ? AF: 0.0757 AC: 11522AN: 152250Hom.: 502 Cov.: 32 AF XY: 0.0741 AC XY: 5517AN XY: 74448
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ClinVar
Significance: Benign/Likely benign
Submissions summary: Benign:3
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
Factor XIII, A subunit, deficiency of Benign:2
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Aug 10, 2021 | - - |
Likely benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jan 13, 2018 | This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as likely benign is not then subjected to further curation. The score for this variant resulted in a classification of likely benign for this disease. - |
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
Computational scores
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BayesDel_noAF
Benign
Cadd
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Dann
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at