rs201000688
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Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_000552.5(VWF):c.5620+50T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0103 in 1,607,146 control chromosomes in the GnomAD database, including 1,308 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.056 ( 729 hom., cov: 32)
Exomes 𝑓: 0.0055 ( 579 hom. )
Consequence
VWF
NM_000552.5 intron
NM_000552.5 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.220
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 Benign. Variant got -14 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.9).
BP6
?
Variant 12-6013431-A-G is Benign according to our data. Variant chr12-6013431-A-G is described in ClinVar as [Benign]. Clinvar id is 256685.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.186 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
VWF | NM_000552.5 | c.5620+50T>C | intron_variant | ENST00000261405.10 | |||
VWF | XM_047429501.1 | c.5620+50T>C | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
VWF | ENST00000261405.10 | c.5620+50T>C | intron_variant | 1 | NM_000552.5 | P1 | |||
VWF | ENST00000538635.5 | n.421-19497T>C | intron_variant, non_coding_transcript_variant | 4 |
Frequencies
GnomAD3 genomes ? AF: 0.0559 AC: 8501AN: 151994Hom.: 731 Cov.: 32
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GnomAD3 exomes AF: 0.0144 AC: 3505AN: 243116Hom.: 268 AF XY: 0.0110 AC XY: 1451AN XY: 132480
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GnomAD4 exome AF: 0.00548 AC: 7979AN: 1455034Hom.: 579 Cov.: 31 AF XY: 0.00475 AC XY: 3437AN XY: 723956
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GnomAD4 genome ? AF: 0.0560 AC: 8520AN: 152112Hom.: 729 Cov.: 32 AF XY: 0.0536 AC XY: 3988AN XY: 74358
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
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
Benign
DANN
Benign
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