rs216293
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Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP4_StrongBS2_Supporting
The NM_000552.5(VWF):c.2282-42C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000476 in 1,602,170 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 0.00035 ( 0 hom., cov: 32)
Exomes 𝑓: 0.00049 ( 0 hom. )
Consequence
VWF
NM_000552.5 intron
NM_000552.5 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.420
Genes affected
VWF (HGNC:12726): (von Willebrand factor) This gene encodes a glycoprotein involved in hemostasis. The encoded preproprotein is proteolytically processed following assembly into large multimeric complexes. These complexes function in the adhesion of platelets to sites of vascular injury and the transport of various proteins in the blood. Mutations in this gene result in von Willebrand disease, an inherited bleeding disorder. An unprocessed pseudogene has been found on chromosome 22. [provided by RefSeq, Oct 2015]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -5 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.84).
BS2
High AC in GnomAd4 at 53 AD gene. Variant has AC lower than other variant known as pathogenic in the gene, so the strength is limited to Supporting.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
VWF | NM_000552.5 | c.2282-42C>G | intron_variant | ENST00000261405.10 | NP_000543.3 | |||
VWF | XM_047429501.1 | c.2282-42C>G | intron_variant | XP_047285457.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
VWF | ENST00000261405.10 | c.2282-42C>G | intron_variant | 1 | NM_000552.5 | ENSP00000261405.5 | ||||
VWF | ENST00000538635.5 | n.421-50559C>G | intron_variant | 4 |
Frequencies
GnomAD3 genomes AF: 0.000349 AC: 53AN: 152016Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.000273 AC: 63AN: 230794Hom.: 0 AF XY: 0.000232 AC XY: 29AN XY: 124928
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GnomAD4 exome AF: 0.000489 AC: 709AN: 1450154Hom.: 0 Cov.: 35 AF XY: 0.000477 AC XY: 344AN XY: 720740
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GnomAD4 genome AF: 0.000349 AC: 53AN: 152016Hom.: 0 Cov.: 32 AF XY: 0.000296 AC XY: 22AN XY: 74222
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ClinVar
Not reported inComputational scores
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Benign
CADD
Benign
DANN
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Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at