rs9315863

Variant names:

• chr13-41735532-G-A
• rs9315863
• NM_015058.2:c.2427-3377C>T

Your query was ambiguous. Multiple possible variants found:

• chr13-41735532-G-A
• chr13-41735532-G-C
• chr13-41735532-G-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_015058.2(VWA8):​c.2427-3377C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.335 in 151,934 control chromosomes in the GnomAD database, including 8,809 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 0.33 (8809 hom., cov: 32)
• Consequence: VWA8 NM_015058.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.590
• Publications: 1 publications found

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]

VWA8 Gene-Disease associations (from GenCC):

• retinitis pigmentosa 97

  Inheritance: AD, Unknown Classification: LIMITED Submitted by: Ambry Genetics, Labcorp Genetics (formerly Invitae)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.367 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
VWA8	NM_015058.2	c.2427-3377C>T		intron_variant	Intron 21 of 44	ENST00000379310.8	NP_055873.1
VWA8	NM_001009814.2	c.2427-3377C>T		intron_variant	Intron 21 of 25		NP_001009814.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
VWA8	ENST00000379310.8	c.2427-3377C>T		intron_variant	Intron 21 of 44	2	NM_015058.2	ENSP00000368612.3
VWA8	ENST00000281496.6	c.2427-3377C>T		intron_variant	Intron 21 of 25	1		ENSP00000281496.6

Frequencies

GnomAD3 genomes AF: 0.335 AC: 50850 AN: 151816 Hom.: 8804 Cov.: 32

Gnomad AFR AF: 0.248

Gnomad AMI AF: 0.253

Gnomad AMR AF: 0.369

Gnomad ASJ AF: 0.479

Gnomad EAS AF: 0.325

Gnomad SAS AF: 0.352

Gnomad FIN AF: 0.356

Gnomad MID AF: 0.293

Gnomad NFE AF: 0.370

Gnomad OTH AF: 0.341

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

GnomAD4 genome AF: 0.335 AC: 50870 AN: 151934 Hom.: 8809 Cov.: 32 AF XY: 0.336 AC XY: 24978 AN XY: 74244

African (AFR) AF: 0.248 AC: 10263 AN: 41454

American (AMR) AF: 0.369 AC: 5636 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.479 AC: 1660 AN: 3468

East Asian (EAS) AF: 0.326 AC: 1685 AN: 5164

South Asian (SAS) AF: 0.352 AC: 1696 AN: 4818

European-Finnish (FIN) AF: 0.356 AC: 3753 AN: 10532

Middle Eastern (MID) AF: 0.298 AC: 87 AN: 292

European-Non Finnish (NFE) AF: 0.370 AC: 25151 AN: 67900

Other (OTH) AF: 0.336 AC: 709 AN: 2110

Alfa AF: 0.298 Hom.: 1609

Bravo AF: 0.333

Asia WGS AF: 0.299 AC: 1037 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	2.0
DANN	Benign	0.55
PhyloP100		0.59
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs9315863; hg19: chr13-42309668;