rs9332684
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBS1BS2
The NM_000130.5(F5):c.250+134A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.019 in 518,024 control chromosomes in the GnomAD database, including 147 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.020 ( 45 hom., cov: 32)
Exomes 𝑓: 0.019 ( 102 hom. )
Consequence
F5
NM_000130.5 intron
NM_000130.5 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -1.24
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 -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.93).
BS1
?
Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0203 (2782/136858) while in subpopulation NFE AF= 0.0245 (1626/66334). AF 95% confidence interval is 0.0235. There are 45 homozygotes in gnomad4. There are 1376 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd4 at 45 AD,AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
F5 | NM_000130.5 | c.250+134A>G | intron_variant | ENST00000367797.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
F5 | ENST00000367797.9 | c.250+134A>G | intron_variant | 1 | NM_000130.5 | P2 | |||
F5 | ENST00000367796.3 | c.250+134A>G | intron_variant | 5 | A2 |
Frequencies
GnomAD3 genomes ? AF: 0.0203 AC: 2780AN: 136776Hom.: 45 Cov.: 32
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GnomAD4 exome AF: 0.0186 AC: 7071AN: 381166Hom.: 102 AF XY: 0.0175 AC XY: 3537AN XY: 202220
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GnomAD4 genome ? AF: 0.0203 AC: 2782AN: 136858Hom.: 45 Cov.: 32 AF XY: 0.0206 AC XY: 1376AN XY: 66756
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
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Prediction
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