22-42020691-G-T

Position:

• chr22-42020691-G-T

Variant summary

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

The NM_152613.3(WBP2NL):​c.406+595G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.816 in 150,344 control chromosomes in the GnomAD database, including 50,702 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 0.82 (50702 hom., cov: 24)
• Consequence: WBP2NL NM_152613.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0450

Genes affected

WBP2NL (HGNC:28389): (WBP2 N-terminal like) WBP2NL is a sperm-specific WW domain-binding protein that promotes meiotic resumption and pronuclear development during oocyte fertilization (Wu et al., 2007 [PubMed 17289678]).[supplied by OMIM, Mar 2008]

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 = 0.934 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
WBP2NL	NM_152613.3	c.406+595G>T		intron_variant		ENST00000328823.13

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
WBP2NL	ENST00000328823.13	c.406+595G>T		intron_variant		1	NM_152613.3	P1

Frequencies

GnomAD3 genomes AF: 0.816 AC: 122636 AN: 150230 Hom.: 50647 Cov.: 24

Gnomad AFR AF: 0.941

Gnomad AMI AF: 0.859

Gnomad AMR AF: 0.787

Gnomad ASJ AF: 0.833

Gnomad EAS AF: 0.905

Gnomad SAS AF: 0.755

Gnomad FIN AF: 0.643

Gnomad MID AF: 0.729

Gnomad NFE AF: 0.771

Gnomad OTH AF: 0.795

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

GnomAD4 genome AF: 0.816 AC: 122744 AN: 150344 Hom.: 50702 Cov.: 24 AF XY: 0.810 AC XY: 59349 AN XY: 73302

Gnomad4 AFR AF: 0.941

Gnomad4 AMR AF: 0.786

Gnomad4 ASJ AF: 0.833

Gnomad4 EAS AF: 0.905

Gnomad4 SAS AF: 0.754

Gnomad4 FIN AF: 0.643

Gnomad4 NFE AF: 0.771

Gnomad4 OTH AF: 0.797

Alfa AF: 0.773 Hom.: 55253

Bravo AF: 0.834

Asia WGS AF: 0.842 AC: 2929 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	1.2
DANN	Benign	0.54

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: rs133337; hg19: chr22-42416695;