rs9532931

chr13-41825943-T-C

Variant summary

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

The NM_015058.2(VWA8):c.1700+4586A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0842 in 152,254 control chromosomes in the GnomAD database, including 556 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 0.084 (556 hom., cov: 32)
• Consequence: VWA8 NM_015058.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.324

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=-0.66).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.102 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
VWA8	NM_015058.2	c.1700+4586A>G		intron_variant		ENST00000379310.8
VWA8	NM_001009814.2	c.1700+4586A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
VWA8	ENST00000379310.8	c.1700+4586A>G		intron_variant		2	NM_015058.2	P1
VWA8	ENST00000281496.6	c.1700+4586A>G		intron_variant		1

Frequencies

GnomAD3 genomes AF: 0.0841 AC: 12802 AN: 152136 Hom.: 554 Cov.: 32

Gnomad AFR AF: 0.0958

Gnomad AMI AF: 0.0835

Gnomad AMR AF: 0.0680

Gnomad ASJ AF: 0.0877

Gnomad EAS AF: 0.110

Gnomad SAS AF: 0.0975

Gnomad FIN AF: 0.0572

Gnomad MID AF: 0.108

Gnomad NFE AF: 0.0815

Gnomad OTH AF: 0.0923

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

GnomAD4 genome AF: 0.0842 AC: 12814 AN: 152254 Hom.: 556 Cov.: 32 AF XY: 0.0836 AC XY: 6225 AN XY: 74440

Gnomad4 AFR AF: 0.0957

Gnomad4 AMR AF: 0.0679

Gnomad4 ASJ AF: 0.0877

Gnomad4 EAS AF: 0.110

Gnomad4 SAS AF: 0.0978

Gnomad4 FIN AF: 0.0572

Gnomad4 NFE AF: 0.0814

Gnomad4 OTH AF: 0.0961

Alfa AF: 0.0831 Hom.: 762

Bravo AF: 0.0849

Asia WGS AF: 0.116 AC: 403 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.66
Cadd	Benign	11
Dann	Benign	0.90

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: rs9532931; hg19: chr13-42400079;