22-42018194-C-T

Variant names:

• chr22-42018194-C-T
• rs4822082
• NM_152613.3:c.63-1117C>T

Variant summary

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

The NM_152613.3(WBP2NL):​c.63-1117C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.777 in 148,344 control chromosomes in the GnomAD database, including 44,850 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 0.78 (44850 hom., cov: 23)
• Consequence: WBP2NL NM_152613.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.737

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=-1.03).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.884 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
WBP2NL	NM_152613.3	c.63-1117C>T		intron_variant	Intron 1 of 5	ENST00000328823.13	NP_689826.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
WBP2NL	ENST00000328823.13	c.63-1117C>T		intron_variant	Intron 1 of 5	1	NM_152613.3	ENSP00000332983.9

Frequencies

GnomAD3 genomes AF: 0.777 AC: 115148 AN: 148256 Hom.: 44827 Cov.: 23

Gnomad AFR AF: 0.801

Gnomad AMI AF: 0.860

Gnomad AMR AF: 0.770

Gnomad ASJ AF: 0.833

Gnomad EAS AF: 0.906

Gnomad SAS AF: 0.755

Gnomad FIN AF: 0.644

Gnomad MID AF: 0.717

Gnomad NFE AF: 0.771

Gnomad OTH AF: 0.767

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

GnomAD4 genome AF: 0.777 AC: 115206 AN: 148344 Hom.: 44850 Cov.: 23 AF XY: 0.771 AC XY: 55638 AN XY: 72204

Gnomad4 AFR AF: 0.801

Gnomad4 AMR AF: 0.769

Gnomad4 ASJ AF: 0.833

Gnomad4 EAS AF: 0.906

Gnomad4 SAS AF: 0.754

Gnomad4 FIN AF: 0.644

Gnomad4 NFE AF: 0.771

Gnomad4 OTH AF: 0.769

Alfa AF: 0.668 Hom.: 1859

Bravo AF: 0.788

Asia WGS AF: 0.822 AC: 2858 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	3.5
DANN	Benign	0.31

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: rs4822082; hg19: chr22-42414198;