3-184233388-G-T
Position:
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_001390846.1(VWA5B2):c.521G>T(p.Cys174Phe) variant causes a missense change. The variant allele was found at a frequency of 0.00000434 in 1,383,026 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: not found (cov: 33)
Exomes 𝑓: 0.0000043 ( 0 hom. )
Consequence
VWA5B2
NM_001390846.1 missense
NM_001390846.1 missense
Scores
2
7
10
Clinical Significance
Conservation
PhyloP100: 6.96
Genes affected
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
VWA5B2 | NM_001390846.1 | c.521G>T | p.Cys174Phe | missense_variant | 4/20 | ENST00000691901.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
VWA5B2 | ENST00000691901.1 | c.521G>T | p.Cys174Phe | missense_variant | 4/20 | NM_001390846.1 | P1 | ||
VWA5B2 | ENST00000426955.6 | c.521G>T | p.Cys174Phe | missense_variant | 3/19 | 1 | P1 | ||
VWA5B2 | ENST00000497229.1 | n.789G>T | non_coding_transcript_exon_variant | 1/3 | 2 | ||||
VWA5B2 | ENST00000273794.5 | upstream_gene_variant | 2 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD3 genomes
Cov.:
33
GnomAD4 exome AF: 0.00000434 AC: 6AN: 1383026Hom.: 0 Cov.: 33 AF XY: 0.00000293 AC XY: 2AN XY: 681580
GnomAD4 exome
AF:
AC:
6
AN:
1383026
Hom.:
Cov.:
33
AF XY:
AC XY:
2
AN XY:
681580
Gnomad4 AFR exome
AF:
Gnomad4 AMR exome
AF:
Gnomad4 ASJ exome
AF:
Gnomad4 EAS exome
AF:
Gnomad4 SAS exome
AF:
Gnomad4 FIN exome
AF:
Gnomad4 NFE exome
AF:
Gnomad4 OTH exome
AF:
GnomAD4 genome Cov.: 33
GnomAD4 genome
Cov.:
33
ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jul 06, 2021 | The c.521G>T (p.C174F) alteration is located in exon 3 (coding exon 3) of the VWA5B2 gene. This alteration results from a G to T substitution at nucleotide position 521, causing the cysteine (C) at amino acid position 174 to be replaced by a phenylalanine (F). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Uncertain
BayesDel_addAF
Uncertain
T
BayesDel_noAF
Benign
CADD
Pathogenic
DANN
Benign
DEOGEN2
Benign
T
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Pathogenic
D
LIST_S2
Benign
T
M_CAP
Benign
T
MetaRNN
Uncertain
T
MetaSVM
Benign
T
MutationAssessor
Uncertain
M
MutationTaster
Benign
D;D
PrimateAI
Pathogenic
D
PROVEAN
Benign
N
REVEL
Benign
Sift
Benign
T
Sift4G
Uncertain
D
Vest4
MutPred
Gain of glycosylation at S177 (P = 0.1202);
MVP
MPC
ClinPred
D
GERP RS
Varity_R
gMVP
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
No publications associated with this variant yet.