rs1800387
Variant summary
Our verdict is Benign. Variant got -19 ACMG points: 1P and 20B. PP2BP4_StrongBP6_Very_StrongBA1
The NM_000552.5(VWF):c.954T>A(p.Asn318Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.051 in 1,613,830 control chromosomes in the GnomAD database, including 8,471 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_000552.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -19 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
VWF | NM_000552.5 | c.954T>A | p.Asn318Lys | missense_variant | 8/52 | ENST00000261405.10 | NP_000543.3 | |
VWF | XM_047429501.1 | c.954T>A | p.Asn318Lys | missense_variant | 8/52 | XP_047285457.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
VWF | ENST00000261405.10 | c.954T>A | p.Asn318Lys | missense_variant | 8/52 | 1 | NM_000552.5 | ENSP00000261405.5 | ||
VWF | ENST00000538635.5 | n.420+36853T>A | intron_variant | 4 |
Frequencies
GnomAD3 genomes AF: 0.143 AC: 21782AN: 151860Hom.: 3879 Cov.: 31
GnomAD3 exomes AF: 0.0612 AC: 15377AN: 251422Hom.: 1752 AF XY: 0.0564 AC XY: 7666AN XY: 135882
GnomAD4 exome AF: 0.0414 AC: 60463AN: 1461852Hom.: 4584 Cov.: 32 AF XY: 0.0416 AC XY: 30246AN XY: 727230
GnomAD4 genome AF: 0.144 AC: 21820AN: 151978Hom.: 3887 Cov.: 31 AF XY: 0.140 AC XY: 10402AN XY: 74304
ClinVar
Submissions by phenotype
not specified Benign:4
Benign, no assertion criteria provided | clinical testing | Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+ | - | - - |
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
Benign, criteria provided, single submitter | clinical testing | Eurofins Ntd Llc (ga) | Dec 22, 2014 | - - |
Benign, no assertion criteria provided | clinical testing | Genome Diagnostics Laboratory, University Medical Center Utrecht | - | - - |
not provided Benign:2
Likely benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jan 29, 2021 | This variant is associated with the following publications: (PMID: 27884173, 24675615) - |
von Willebrand disease type 2 Benign:1
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Dec 05, 2021 | - - |
von Willebrand disease type 3 Benign:1
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Dec 05, 2021 | - - |
von Willebrand disease type 1 Benign:1
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Dec 05, 2021 | - - |
Hereditary von Willebrand disease Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jun 14, 2016 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at