chr13-41670999-G-A
Variant summary
Our verdict is Likely benign. Variant got -1 ACMG points: 3P and 4B. PM4PP5BS2
The NM_015058.2(VWA8):c.4558C>T(p.Arg1520Ter) variant causes a stop gained change. The variant allele was found at a frequency of 0.0000136 in 1,613,714 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Likely pathogenic (no stars). Variant results in nonsense mediated mRNA decay.
Frequency
Genomes: 𝑓 0.000033 ( 0 hom., cov: 32)
Exomes 𝑓: 0.000012 ( 0 hom. )
Consequence
VWA8
NM_015058.2 stop_gained
NM_015058.2 stop_gained
Scores
3
3
1
Clinical Significance
Conservation
PhyloP100: 5.68
Genes affected
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -1 ACMG points.
PM4
?
Stoplost variant in NM_015058.2 Downstream stopcodon found after 48 codons.
PP5
?
Variant 13-41670999-G-A is Pathogenic according to our data. Variant chr13-41670999-G-A is described in ClinVar as [Likely_pathogenic]. Clinvar id is 617838.Status of the report is no_assertion_criteria_provided, 0 stars.
BS2
?
High AC in GnomAd at 5 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
VWA8 | NM_015058.2 | c.4558C>T | p.Arg1520Ter | stop_gained | 37/45 | ENST00000379310.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
VWA8 | ENST00000379310.8 | c.4558C>T | p.Arg1520Ter | stop_gained | 37/45 | 2 | NM_015058.2 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000329 AC: 5AN: 152042Hom.: 0 Cov.: 32
GnomAD3 genomes
?
AF:
AC:
5
AN:
152042
Hom.:
Cov.:
32
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD3 exomes AF: 0.0000120 AC: 3AN: 249498Hom.: 0 AF XY: 0.0000222 AC XY: 3AN XY: 135366
GnomAD3 exomes
AF:
AC:
3
AN:
249498
Hom.:
AF XY:
AC XY:
3
AN XY:
135366
Gnomad AFR exome
AF:
Gnomad AMR exome
AF:
Gnomad ASJ exome
AF:
Gnomad EAS exome
AF:
Gnomad SAS exome
AF:
Gnomad FIN exome
AF:
Gnomad NFE exome
AF:
Gnomad OTH exome
AF:
GnomAD4 exome AF: 0.0000116 AC: 17AN: 1461672Hom.: 0 Cov.: 31 AF XY: 0.0000151 AC XY: 11AN XY: 727158
GnomAD4 exome
AF:
AC:
17
AN:
1461672
Hom.:
Cov.:
31
AF XY:
AC XY:
11
AN XY:
727158
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 ? AF: 0.0000329 AC: 5AN: 152042Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74272
GnomAD4 genome
?
AF:
AC:
5
AN:
152042
Hom.:
Cov.:
32
AF XY:
AC XY:
1
AN XY:
74272
Gnomad4 AFR
AF:
Gnomad4 AMR
AF:
Gnomad4 ASJ
AF:
Gnomad4 EAS
AF:
Gnomad4 SAS
AF:
Gnomad4 FIN
AF:
Gnomad4 NFE
AF:
Gnomad4 OTH
AF:
Bravo
AF:
ESP6500AA
AF:
AC:
0
ESP6500EA
AF:
AC:
1
ExAC
?
AF:
AC:
1
EpiCase
AF:
EpiControl
AF:
ClinVar
Significance: Likely pathogenic
Submissions summary: Pathogenic:1
Revision: no assertion criteria provided
LINK: link
Submissions by phenotype
Nonsyndromic cleft lip palate Pathogenic:1
Likely pathogenic, no assertion criteria provided | research | University of Washington Center for Mendelian Genomics, University of Washington | Mar 27, 2016 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_addAF
Pathogenic
D
BayesDel_noAF
Pathogenic
Cadd
Pathogenic
Dann
Uncertain
Eigen
Pathogenic
Eigen_PC
Uncertain
FATHMM_MKL
Uncertain
D
MutationTaster
Benign
A;A
Vest4
GERP RS
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at