rs216901

chr12-5995702-G-A

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The NM_000552.5(VWF):c.6063+300C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.517 in 152,000 control chromosomes in the GnomAD database, including 20,711 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.52 (20711 hom., cov: 31)
• Consequence: VWF NM_000552.5 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.191

Genes affected

VWF (HGNC:12726): (von Willebrand factor) This gene encodes a glycoprotein involved in hemostasis. The encoded preproprotein is proteolytically processed following assembly into large multimeric complexes. These complexes function in the adhesion of platelets to sites of vascular injury and the transport of various proteins in the blood. Mutations in this gene result in von Willebrand disease, an inherited bleeding disorder. An unprocessed pseudogene has been found on chromosome 22. [provided by RefSeq, Oct 2015]

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BP6: Variant 12-5995702-G-A is Benign according to our data. Variant chr12-5995702-G-A is described in ClinVar as [Benign]. Clinvar id is 1182188.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.728 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
VWF	NM_000552.5	c.6063+300C>T		intron_variant		ENST00000261405.10
VWF	XM_047429501.1	c.6063+300C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
VWF	ENST00000261405.10	c.6063+300C>T		intron_variant		1	NM_000552.5	P1
VWF	ENST00000538635.5	n.421-1768C>T		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.517 AC: 78534 AN: 151882 Hom.: 20690 Cov.: 31

Gnomad AFR AF: 0.443

Gnomad AMI AF: 0.500

Gnomad AMR AF: 0.576

Gnomad ASJ AF: 0.478

Gnomad EAS AF: 0.746

Gnomad SAS AF: 0.594

Gnomad FIN AF: 0.500

Gnomad MID AF: 0.413

Gnomad NFE AF: 0.531

Gnomad OTH AF: 0.514

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

GnomAD4 genome AF: 0.517 AC: 78592 AN: 152000 Hom.: 20711 Cov.: 31 AF XY: 0.520 AC XY: 38637 AN XY: 74292

Gnomad4 AFR AF: 0.443

Gnomad4 AMR AF: 0.576

Gnomad4 ASJ AF: 0.478

Gnomad4 EAS AF: 0.747

Gnomad4 SAS AF: 0.593

Gnomad4 FIN AF: 0.500

Gnomad4 NFE AF: 0.531

Gnomad4 OTH AF: 0.517

Alfa AF: 0.525 Hom.: 2628

Bravo AF: 0.516

Asia WGS AF: 0.620 AC: 2157 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Nov 12, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	2.0
Dann	Benign	0.56

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

Other links and lift over

dbSNP: rs216901; hg19: chr12-6104868;