7-49902109-T-C

Position:

• chr7-49902109-T-C

Variant summary

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

The NM_198570.5(VWC2):​c.827-9925T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.737 in 151,700 control chromosomes in the GnomAD database, including 41,359 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 0.74 (41359 hom., cov: 31)
• Consequence: VWC2 NM_198570.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.208

Genes affected

VWC2 (HGNC:30200): (von Willebrand factor C domain containing 2) This gene encodes a secreted bone morphogenic protein antagonist. The encoded protein is possibly involved in neural function and development and may have a role in cell adhesion.[provided by RefSeq, Oct 2009]

ZPBP (HGNC:15662): (zona pellucida binding protein) ZPBP is one of several proteins that are thought to participate in secondary binding between acrosome-reacted sperm and the egg-specific extracellular matrix, the zona pellucida (McLeskey et al., 1998 [PubMed 9378618]).[supplied by OMIM, Aug 2008]

ZPBP (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.864 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
VWC2	NM_198570.5	c.827-9925T>C		intron_variant		ENST00000340652.5	NP_940972.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
VWC2	ENST00000340652.5	c.827-9925T>C		intron_variant		1	NM_198570.5	ENSP00000341819.3
ZPBP	ENST00000465922.1	n.412-894A>G		intron_variant		4
ZPBP	ENST00000491129.5	n.419-894A>G		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.737 AC: 111660 AN: 151582 Hom.: 41340 Cov.: 31

Gnomad AFR AF: 0.708

Gnomad AMI AF: 0.831

Gnomad AMR AF: 0.649

Gnomad ASJ AF: 0.695

Gnomad EAS AF: 0.885

Gnomad SAS AF: 0.696

Gnomad FIN AF: 0.816

Gnomad MID AF: 0.741

Gnomad NFE AF: 0.755

Gnomad OTH AF: 0.717

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

GnomAD4 genome AF: 0.737 AC: 111732 AN: 151700 Hom.: 41359 Cov.: 31 AF XY: 0.739 AC XY: 54785 AN XY: 74110

Gnomad4 AFR AF: 0.707

Gnomad4 AMR AF: 0.649

Gnomad4 ASJ AF: 0.695

Gnomad4 EAS AF: 0.885

Gnomad4 SAS AF: 0.697

Gnomad4 FIN AF: 0.816

Gnomad4 NFE AF: 0.755

Gnomad4 OTH AF: 0.716

Alfa AF: 0.722 Hom.: 6019

Bravo AF: 0.722

Asia WGS AF: 0.734 AC: 2546 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	5.8
DANN	Benign	0.78

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: rs1532989; hg19: chr7-49941705;