Variant rs880321 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001130142.2(VWA5A):c.931-65T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.1 in 1,541,612 control chromosomes in the GnomAD database, including 8,421 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 0.083 ( 608 hom., cov: 32)

Exomes 𝑓: 0.10 ( 7813 hom. )

Consequence

VWA5A
NM_001130142.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.582

Variant links:

Genes affected

VWA5A (HGNC:6658): (von Willebrand factor A domain containing 5A) Located in nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]

VWA5A links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -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 = 0.107 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	MANE	Protein	UniProt
VWA5A	NM_001130142.2 link	c.931-65T>C	intron_variant	ENST00000456829.7	NP_001123614.1	O00534-1A0A024R3H3
VWA5A	NM_014622.5 link	c.931-65T>C	intron_variant		NP_055437.2	O00534-1A0A024R3H3
VWA5A	NM_198315.3 link	c.931-65T>C	intron_variant		NP_938057.1	O00534-3
VWA5A	XM_011542828.3 link	c.979-65T>C	intron_variant		XP_011541130.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
VWA5A	ENST00000456829.7 link	c.931-65T>C		intron_variant		1	NM_001130142.2	ENSP00000407726.2		O00534-1

Frequencies

GnomAD3 genomes

AF:

0.0828

AC:

12581

AN:

152036

Hom.:

610

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0497

Gnomad AMI

AF:

0.0340

Gnomad AMR

AF:

0.0655

Gnomad ASJ

AF:

0.0613

Gnomad EAS

AF:

0.0358

Gnomad SAS

AF:

0.104

Gnomad FIN

AF:

0.0917

Gnomad MID

AF:

0.0475

Gnomad NFE

AF:

0.109

Gnomad OTH

AF:

0.0866

GnomAD4 exome

AF:

0.102

AC:

142045

AN:

1389458

Hom.:

7813

Cov.:

AF XY:

0.102

AC XY:

70947

AN XY:

693076

show subpopulations

Gnomad4 AFR exome

AF:

0.0461

Gnomad4 AMR exome

AF:

0.0534

Gnomad4 ASJ exome

AF:

0.0525

Gnomad4 EAS exome

AF:

0.0536

Gnomad4 SAS exome

AF:

0.0989

Gnomad4 FIN exome

AF:

0.102

Gnomad4 NFE exome

AF:

0.110

Gnomad4 OTH exome

AF:

0.0939

GnomAD4 genome

AF:

0.0827

AC:

12582

AN:

152154

Hom.:

608

Cov.:

AF XY:

0.0801

AC XY:

5956

AN XY:

74390

show subpopulations

Gnomad4 AFR

AF:

0.0497

Gnomad4 AMR

AF:

0.0654

Gnomad4 ASJ

AF:

0.0613

Gnomad4 EAS

AF:

0.0359

Gnomad4 SAS

AF:

0.104

Gnomad4 FIN

AF:

0.0917

Gnomad4 NFE

AF:

0.109

Gnomad4 OTH

AF:

0.0857

Alfa

AF:

0.0988

Hom.:

418

Bravo

AF:

0.0787

Asia WGS

AF:

0.0710

AC:

249

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.82

CADD

Benign

6.0

DANN

Benign

0.53

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over