chr12-5949041-A-G

Variant summary

Our verdict is Likely pathogenic. Variant got 7 ACMG points: 7P and 0B. PM2PP2PP3_Strong

The NM_000552.5(VWF):​c.8416T>C​(p.Cys2806Arg) variant causes a missense change. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★★).

Frequency

Genomes: not found (cov: 33)

Consequence

VWF
NM_000552.5 missense

Scores

11
5
3

Clinical Significance

Uncertain significance criteria provided, multiple submitters, no conflicts U:2O:1

Conservation

PhyloP100: 6.69
Variant links:
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_pathogenic. Variant got 7 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
PP2
Missense variant in the VWF gene, where missense mutations are typically associated with disease (based on misZ statistic). The gene has 149 curated pathogenic missense variants (we use a threshold of 10). The gene has 28 curated benign missense variants. Gene score misZ: 0.98969 (below the threshold of 3.09). Trascript score misZ: 3.5064 (above the threshold of 3.09). GenCC associations: The gene is linked to von Willebrand disease type 2M, hereditary von Willebrand disease, von Willebrand disease type 2B, von Willebrand disease type 2N, von Willebrand disease 2, von Willebrand disease type 2A, von Willebrand disease 3, von Willebrand disease 1.
PP3
MetaRNN computational evidence supports a deleterious effect, 0.943

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
VWFNM_000552.5 linkc.8416T>C p.Cys2806Arg missense_variant Exon 52 of 52 ENST00000261405.10 NP_000543.3 P04275-1
VWFXM_047429501.1 linkc.8416T>C p.Cys2806Arg missense_variant Exon 52 of 52 XP_047285457.1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
VWFENST00000261405.10 linkc.8416T>C p.Cys2806Arg missense_variant Exon 52 of 52 1 NM_000552.5 ENSP00000261405.5 P04275-1

Frequencies

GnomAD3 genomes
Cov.:
33
GnomAD4 exome
Cov.:
31
GnomAD4 genome
Cov.:
33

ClinVar

Significance: Uncertain significance
Submissions summary: Uncertain:2Other:1
Revision: criteria provided, multiple submitters, no conflicts
LINK: link

Submissions by phenotype

not provided Uncertain:2Other:1
-
Academic Unit of Haematology, University of Sheffield
Significance: not provided
Review Status: no classification provided
Collection Method: literature only

- -

Jun 17, 2021
Quest Diagnostics Nichols Institute San Juan Capistrano
Significance: Uncertain significance
Review Status: criteria provided, single submitter
Collection Method: clinical testing

- -

Jan 04, 2023
ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories
Significance: Uncertain significance
Review Status: criteria provided, single submitter
Collection Method: clinical testing

The VWF c.8416T>C; p.Cys2806Arg variant (rs267607372), to our knowledge, is not reported in the medical literature but is reported in the Hemobase VWF database (see link). This variant is reported in ClinVar (Variation ID: 100509) and is absent from the Genome Aggregation Database, indicating it is not a common polymorphism. The cysteine at codon 2806 is highly conserved, and computational analyses predict that this variant is deleterious (REVEL: 0.789). However, given the lack of clinical and functional data, the significance of the p.Cys2806Arg variant is uncertain at this time. References: Hemobase VWF database: http://vwf.hemobase.com/VWF_Database/VWF_Database.htm -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
0.90
BayesDel_addAF
Pathogenic
0.44
D
BayesDel_noAF
Pathogenic
0.40
CADD
Uncertain
24
DANN
Benign
0.84
DEOGEN2
Pathogenic
0.85
D
Eigen
Uncertain
0.55
Eigen_PC
Uncertain
0.37
FATHMM_MKL
Uncertain
0.89
D
LIST_S2
Benign
0.76
T
M_CAP
Pathogenic
0.69
D
MetaRNN
Pathogenic
0.94
D
MetaSVM
Uncertain
0.76
D
MutationAssessor
Pathogenic
3.6
H
PrimateAI
Uncertain
0.58
T
PROVEAN
Pathogenic
-5.3
D
REVEL
Pathogenic
0.79
Sift
Pathogenic
0.0
D
Sift4G
Pathogenic
0.0
D
Polyphen
1.0
D
Vest4
0.96
MutPred
0.54
Gain of catalytic residue at M2802 (P = 0);
MVP
0.93
MPC
1.1
ClinPred
0.94
D
GERP RS
5.3
Varity_R
0.94
gMVP
1.0

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs267607372; hg19: chr12-6058207; API