rs707928

chr6-31774813-A-Gchr6-31774813-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_025258.3(VWA7):c.611-187T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.464 in 151,932 control chromosomes in the GnomAD database, including 18,317 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 0.46 (18317 hom., cov: 31)
• Consequence: VWA7 NM_025258.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.161

Genes affected

VWA7 (HGNC:13939): (von Willebrand factor A domain containing 7) Predicted to be located in extracellular region. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.705 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
VWA7	NM_025258.3	c.611-187T>C		intron_variant		ENST00000375688.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
VWA7	ENST00000375688.5	c.611-187T>C		intron_variant		5	NM_025258.3	P1
VWA7	ENST00000467576.1	n.590-187T>C		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.463 AC: 70352 AN: 151814 Hom.: 18280 Cov.: 31

Gnomad AFR AF: 0.712

Gnomad AMI AF: 0.264

Gnomad AMR AF: 0.455

Gnomad ASJ AF: 0.312

Gnomad EAS AF: 0.386

Gnomad SAS AF: 0.428

Gnomad FIN AF: 0.451

Gnomad MID AF: 0.424

Gnomad NFE AF: 0.335

Gnomad OTH AF: 0.460

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

GnomAD4 genome AF: 0.464 AC: 70442 AN: 151932 Hom.: 18317 Cov.: 31 AF XY: 0.466 AC XY: 34562 AN XY: 74224

Gnomad4 AFR AF: 0.712

Gnomad4 AMR AF: 0.455

Gnomad4 ASJ AF: 0.312

Gnomad4 EAS AF: 0.387

Gnomad4 SAS AF: 0.427

Gnomad4 FIN AF: 0.451

Gnomad4 NFE AF: 0.335

Gnomad4 OTH AF: 0.463

Alfa AF: 0.355 Hom.: 18849

Bravo AF: 0.474

Asia WGS AF: 0.514 AC: 1782 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
Cadd	Benign	1.7
Dann	Benign	0.36

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs707928; hg19: chr6-31742590;