dbSNP rs4936894: VWA5A:c.*841G>A (chr11-124146786-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_001130142.2(VWA5A):c.*841G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.188 in 152,364 control chromosomes in the GnomAD database, including 3,265 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 0.19 ( 3256 hom., cov: 31)

Exomes 𝑓: 0.24 ( 9 hom. )

Consequence

VWA5A
NM_001130142.2 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -3.54

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:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-1.02).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.448 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	MANE	Protein	UniProt
VWA5A	NM_001130142.2 link	c.*841G>A	3_prime_UTR_variant	Exon 19 of 19	ENST00000456829.7	NP_001123614.1	O00534-1A0A024R3H3
VWA5A	NM_014622.5 link	c.*841G>A	3_prime_UTR_variant	Exon 18 of 18		NP_055437.2	O00534-1A0A024R3H3
VWA5A	XM_011542828.3 link	c.*841G>A	3_prime_UTR_variant	Exon 19 of 19		XP_011541130.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
VWA5A	ENST00000456829.7 link	c.*841G>A		3_prime_UTR_variant	Exon 19 of 19	1	NM_001130142.2	ENSP00000407726.2		O00534-1
VWA5A	ENST00000392748.5 link	c.*841G>A		3_prime_UTR_variant	Exon 18 of 18	1		ENSP00000376504.1		O00534-1

Frequencies

GnomAD3 genomes

AF:

0.188

AC:

28502

AN:

151922

Hom.:

3260

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0707

Gnomad AMI

AF:

0.130

Gnomad AMR

AF:

0.259

Gnomad ASJ

AF:

0.218

Gnomad EAS

AF:

0.463

Gnomad SAS

AF:

0.142

Gnomad FIN

AF:

0.202

Gnomad MID

AF:

0.111

Gnomad NFE

AF:

0.222

Gnomad OTH

AF:

0.188

GnomAD4 exome

AF:

0.238

AC:

AN:

324

Hom.:

Cov.:

AF XY:

0.235

AC XY:

AN XY:

162

show subpopulations

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 FIN exome

AF:

0.247

Gnomad4 NFE exome

AF:

0.167

Gnomad4 OTH exome

AF:

0.250

GnomAD4 genome

AF:

0.188

AC:

28508

AN:

152040

Hom.:

3256

Cov.:

AF XY:

0.191

AC XY:

14194

AN XY:

74308

show subpopulations

Gnomad4 AFR

AF:

0.0707

Gnomad4 AMR

AF:

0.259

Gnomad4 ASJ

AF:

0.218

Gnomad4 EAS

AF:

0.464

Gnomad4 SAS

AF:

0.143

Gnomad4 FIN

AF:

0.202

Gnomad4 NFE

AF:

0.222

Gnomad4 OTH

AF:

0.188

Alfa

AF:

0.217

Hom.:

8115

Bravo

AF:

0.186

Asia WGS

AF:

0.238

AC:

828

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.0

CADD

Benign

0.046

DANN

Benign

0.47

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