rs9566867

chr13-41854763-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_015058.2(VWA8):c.1425+10973C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0612 in 152,268 control chromosomes in the GnomAD database, including 359 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.061 (359 hom., cov: 31)
• Consequence: VWA8 NM_015058.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.470

Genes affected

VWA8 (HGNC:29071): (von Willebrand factor A domain containing 8) Predicted to enable ATP binding activity. Located in mitochondrion and peroxisome. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.65).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.108 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
VWA8	NM_015058.2	c.1425+10973C>T		intron_variant		ENST00000379310.8
VWA8	NM_001009814.2	c.1425+10973C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
VWA8	ENST00000379310.8	c.1425+10973C>T		intron_variant		2	NM_015058.2	P1
VWA8	ENST00000281496.6	c.1425+10973C>T		intron_variant		1

Frequencies

GnomAD3 genomes AF: 0.0612 AC: 9309 AN: 152150 Hom.: 354 Cov.: 31

Gnomad AFR AF: 0.0999

Gnomad AMI AF: 0.0362

Gnomad AMR AF: 0.0554

Gnomad ASJ AF: 0.0913

Gnomad EAS AF: 0.115

Gnomad SAS AF: 0.0381

Gnomad FIN AF: 0.0332

Gnomad MID AF: 0.0665

Gnomad NFE AF: 0.0398

Gnomad OTH AF: 0.0556

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0612 AC: 9323 AN: 152268 Hom.: 359 Cov.: 31 AF XY: 0.0600 AC XY: 4470 AN XY: 74454

Gnomad4 AFR AF: 0.0997

Gnomad4 AMR AF: 0.0559

Gnomad4 ASJ AF: 0.0913

Gnomad4 EAS AF: 0.115

Gnomad4 SAS AF: 0.0381

Gnomad4 FIN AF: 0.0332

Gnomad4 NFE AF: 0.0398

Gnomad4 OTH AF: 0.0550

Alfa AF: 0.0535 Hom.: 38

Bravo AF: 0.0644

Asia WGS AF: 0.0790 AC: 273 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.65
Cadd	Benign	12
Dann	Benign	0.84

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

Other links and lift over

dbSNP: rs9566867; hg19: chr13-42428899;