Variant 13-41721523-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2

The NM_015058.2(VWA8):c.2811C>T(p.Leu937=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00606 in 1,613,768 control chromosomes in the GnomAD database, including 56 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.0048 ( 7 hom., cov: 32)

Exomes 𝑓: 0.0062 ( 49 hom. )

Consequence

VWA8
NM_015058.2 synonymous

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -1.81

Variant links:

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 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -11 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.71).

BP6

Variant 13-41721523-G-A is Benign according to our data. Variant chr13-41721523-G-A is described in ClinVar as [Benign]. Clinvar id is 784677.Status of the report is criteria_provided_single_submitter, 1 stars.

BP7

Synonymous conserved (PhyloP=-1.81 with no splicing effect.

BS2

High AC in GnomAd4 at 727 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
VWA8	NM_015058.2 linkuse as main transcript	c.2811C>T	p.Leu937=	synonymous_variant	25/45	ENST00000379310.8
VWA8	NM_001009814.2 linkuse as main transcript	c.2811C>T	p.Leu937=	synonymous_variant	25/26

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
VWA8	ENST00000379310.8 linkuse as main transcript	c.2811C>T	p.Leu937=	synonymous_variant	25/45	2	NM_015058.2	P1	A3KMH1-1
VWA8	ENST00000281496.6 linkuse as main transcript	c.2811C>T	p.Leu937=	synonymous_variant	25/26	1			A3KMH1-2

Frequencies

GnomAD3 genomes

AF:

0.00479

AC:

728

AN:

152128

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000821

Gnomad AMI

AF:

0.0253

Gnomad AMR

AF:

0.00367

Gnomad ASJ

AF:

0.00982

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.000415

Gnomad FIN

AF:

0.00132

Gnomad MID

AF:

0.00633

Gnomad NFE

AF:

0.00800

Gnomad OTH

AF:

0.00911

GnomAD3 exomes

AF:

0.00451

AC:

1132

AN:

250838

Hom.:

AF XY:

0.00462

AC XY:

626

AN XY:

135542

show subpopulations

Gnomad AFR exome

AF:

0.00105

Gnomad AMR exome

AF:

0.00243

Gnomad ASJ exome

AF:

0.0116

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.000392

Gnomad FIN exome

AF:

0.00111

Gnomad NFE exome

AF:

0.00733

Gnomad OTH exome

AF:

0.00768

GnomAD4 exome

AF:

0.00620

AC:

9059

AN:

1461522

Hom.:

Cov.:

AF XY:

0.00617

AC XY:

4489

AN XY:

727062

show subpopulations

Gnomad4 AFR exome

AF:

0.000777

Gnomad4 AMR exome

AF:

0.00273

Gnomad4 ASJ exome

AF:

0.0115

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.000672

Gnomad4 FIN exome

AF:

0.00109

Gnomad4 NFE exome

AF:

0.00726

Gnomad4 OTH exome

AF:

0.00575

GnomAD4 genome

AF:

0.00478

AC:

727

AN:

152246

Hom.:

Cov.:

AF XY:

0.00455

AC XY:

339

AN XY:

74444

show subpopulations

Gnomad4 AFR

AF:

0.000818

Gnomad4 AMR

AF:

0.00366

Gnomad4 ASJ

AF:

0.00982

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.000415

Gnomad4 FIN

AF:

0.00132

Gnomad4 NFE

AF:

0.00798

Gnomad4 OTH

AF:

0.00901

Alfa

AF:

0.00552

Hom.:

Bravo

AF:

0.00484

Asia WGS

AF:

0.000289

AC:

AN:

3476

EpiCase

AF:

0.00786

EpiControl

AF:

0.00741

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

Invitae

May 09, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.71

CADD

Benign

0.75

DANN

Benign

0.60

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over