rs7545236
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Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The ENST00000367797.9(F5):c.374-66T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.211 in 1,416,802 control chromosomes in the GnomAD database, including 42,645 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.33 ( 10859 hom., cov: 32)
Exomes 𝑓: 0.20 ( 31786 hom. )
Consequence
F5
ENST00000367797.9 intron
ENST00000367797.9 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: 1.31
Genes affected
F5 (HGNC:3542): (coagulation factor V) This gene encodes an essential cofactor of the blood coagulation cascade. This factor circulates in plasma, and is converted to the active form by the release of the activation peptide by thrombin during coagulation. This generates a heavy chain and a light chain which are held together by calcium ions. The activated protein is a cofactor that participates with activated coagulation factor X to activate prothrombin to thrombin. Defects in this gene result in either an autosomal recessive hemorrhagic diathesis or an autosomal dominant form of thrombophilia, which is known as activated protein C resistance. [provided by RefSeq, Oct 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -20 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.83).
BP6
Variant 1-169560832-A-C is Benign according to our data. Variant chr1-169560832-A-C is described in ClinVar as [Benign]. Clinvar id is 1286244.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.633 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
F5 | NM_000130.5 | c.374-66T>G | intron_variant | ENST00000367797.9 | NP_000121.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
F5 | ENST00000367797.9 | c.374-66T>G | intron_variant | 1 | NM_000130.5 | ENSP00000356771 | P2 | |||
F5 | ENST00000367796.3 | c.374-66T>G | intron_variant | 5 | ENSP00000356770 | A2 |
Frequencies
GnomAD3 genomes AF: 0.326 AC: 49561AN: 151802Hom.: 10837 Cov.: 32
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GnomAD4 exome AF: 0.197 AC: 248991AN: 1264882Hom.: 31786 AF XY: 0.195 AC XY: 124318AN XY: 638590
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GnomAD4 genome AF: 0.327 AC: 49632AN: 151920Hom.: 10859 Cov.: 32 AF XY: 0.328 AC XY: 24397AN XY: 74280
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ClinVar
Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Nov 10, 2018 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at