rs133333

Positions:

• chr22-42016361-G-A

Variant summary

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

The NM_152613.3(WBP2NL):​c.63-2950G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.722 in 151,956 control chromosomes in the GnomAD database, including 40,087 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 0.72 (40087 hom., cov: 30)
• Consequence: WBP2NL NM_152613.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.686

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]

WBP2NL (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.883 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
WBP2NL	NM_152613.3	c.63-2950G>A		intron_variant		ENST00000328823.13	NP_689826.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
WBP2NL	ENST00000328823.13	c.63-2950G>A		intron_variant		1	NM_152613.3	ENSP00000332983.9

Frequencies

GnomAD3 genomes AF: 0.722 AC: 109669 AN: 151836 Hom.: 40073 Cov.: 30

Gnomad AFR AF: 0.621

Gnomad AMI AF: 0.856

Gnomad AMR AF: 0.751

Gnomad ASJ AF: 0.789

Gnomad EAS AF: 0.905

Gnomad SAS AF: 0.750

Gnomad FIN AF: 0.646

Gnomad MID AF: 0.649

Gnomad NFE AF: 0.768

Gnomad OTH AF: 0.730

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

GnomAD4 genome AF: 0.722 AC: 109724 AN: 151956 Hom.: 40087 Cov.: 30 AF XY: 0.718 AC XY: 53329 AN XY: 74256

Gnomad4 AFR AF: 0.621

Gnomad4 AMR AF: 0.751

Gnomad4 ASJ AF: 0.789

Gnomad4 EAS AF: 0.905

Gnomad4 SAS AF: 0.749

Gnomad4 FIN AF: 0.646

Gnomad4 NFE AF: 0.768

Gnomad4 OTH AF: 0.732

Alfa AF: 0.753 Hom.: 19905

Bravo AF: 0.728

Asia WGS AF: 0.811 AC: 2823 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.46
DANN	Benign	0.68

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: rs133333; hg19: chr22-42412365;