chr22-42020691-G-T

Variant names:

• chr22-42020691-G-T
• rs133337
• NM_152613.3:c.406+595G>T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 16 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_152613.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	WBP2NL	NM_152613.3	MANE Select	c.406+595G>T		intron	N/A	NP_689826.2	Q6ICG8

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	WBP2NL	ENST00000328823.13	TSL:1 MANE Select	c.406+595G>T		intron	N/A	ENSP00000332983.9	Q6ICG8
	WBP2NL	ENST00000943073.1		c.406+595G>T		intron	N/A	ENSP00000613132.1
	WBP2NL	ENST00000329620.9	TSL:2	n.406+595G>T		intron	N/A	ENSP00000328800.5	Q6ICG8

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

African (AFR) AF: 0.941 AC: 38604 AN: 41008

American (AMR) AF: 0.786 AC: 11778 AN: 14980

Ashkenazi Jewish (ASJ) AF: 0.833 AC: 2881 AN: 3460

East Asian (EAS) AF: 0.905 AC: 4585 AN: 5064

South Asian (SAS) AF: 0.754 AC: 3575 AN: 4744

European-Finnish (FIN) AF: 0.643 AC: 6520 AN: 10134

Middle Eastern (MID) AF: 0.729 AC: 213 AN: 292

European-Non Finnish (NFE) AF: 0.771 AC: 52146 AN: 67668

Other (OTH) AF: 0.797 AC: 1662 AN: 2086

Alfa AF: 0.780 Hom.: 72675

Bravo AF: 0.834

Asia WGS AF: 0.842 AC: 2929 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.2
DANN	Benign	0.54
PhyloP100		-0.045
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs133337; hg19: chr22-42416695;