rs9590614

chr13-41601452-G-Cchr13-41601452-G-T

Variant summary

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

The NM_015058.2(VWA8):c.4986+3716C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.308 in 151,972 control chromosomes in the GnomAD database, including 7,963 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 0.31 (7963 hom., cov: 32)
• Consequence: VWA8 NM_015058.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.17

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=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.381 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
VWA8	NM_015058.2	c.4986+3716C>G		intron_variant		ENST00000379310.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
VWA8	ENST00000379310.8	c.4986+3716C>G		intron_variant		2	NM_015058.2	P1

Frequencies

GnomAD3 genomes AF: 0.309 AC: 46851 AN: 151854 Hom.: 7962 Cov.: 32

Gnomad AFR AF: 0.162

Gnomad AMI AF: 0.305

Gnomad AMR AF: 0.329

Gnomad ASJ AF: 0.410

Gnomad EAS AF: 0.169

Gnomad SAS AF: 0.357

Gnomad FIN AF: 0.370

Gnomad MID AF: 0.244

Gnomad NFE AF: 0.385

Gnomad OTH AF: 0.326

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

GnomAD4 genome AF: 0.308 AC: 46851 AN: 151972 Hom.: 7963 Cov.: 32 AF XY: 0.309 AC XY: 22963 AN XY: 74288

Gnomad4 AFR AF: 0.162

Gnomad4 AMR AF: 0.328

Gnomad4 ASJ AF: 0.410

Gnomad4 EAS AF: 0.169

Gnomad4 SAS AF: 0.359

Gnomad4 FIN AF: 0.370

Gnomad4 NFE AF: 0.385

Gnomad4 OTH AF: 0.322

Alfa AF: 0.222 Hom.: 525

Bravo AF: 0.298

Asia WGS AF: 0.233 AC: 811 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
Cadd	Benign	8.8
Dann	Benign	0.71

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs9590614; hg19: chr13-42175588;