chr13-41615006-C-T
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 2P and 10B. PM5BP4_StrongBP6_ModerateBS2
The NM_015058.2(VWA8):c.4690G>A(p.Val1564Met) variant causes a missense change. The variant allele was found at a frequency of 0.00662 in 1,613,696 control chromosomes in the GnomAD database, including 40 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. V1564L) has been classified as Likely pathogenic.
Frequency
Consequence
NM_015058.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
VWA8 | NM_015058.2 | c.4690G>A | p.Val1564Met | missense_variant | 38/45 | ENST00000379310.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
VWA8 | ENST00000379310.8 | c.4690G>A | p.Val1564Met | missense_variant | 38/45 | 2 | NM_015058.2 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00457 AC: 695AN: 152158Hom.: 2 Cov.: 32
GnomAD3 exomes AF: 0.00456 AC: 1137AN: 249350Hom.: 5 AF XY: 0.00465 AC XY: 629AN XY: 135286
GnomAD4 exome AF: 0.00684 AC: 9993AN: 1461420Hom.: 38 Cov.: 30 AF XY: 0.00666 AC XY: 4839AN XY: 727038
GnomAD4 genome ? AF: 0.00456 AC: 694AN: 152276Hom.: 2 Cov.: 32 AF XY: 0.00445 AC XY: 331AN XY: 74458
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Nov 01, 2023 | VWA8: PM5, BS2 - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at