22-42000367-G-A

Position:

• chr22-42000367-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.62+1487G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.292 in 152,060 control chromosomes in the GnomAD database, including 6,957 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 0.29 (6957 hom., cov: 32)
• Consequence: WBP2NL NM_152613.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.11

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=-0.92).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.359 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
WBP2NL	NM_152613.3	c.62+1487G>A		intron_variant		ENST00000328823.13

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
WBP2NL	ENST00000328823.13	c.62+1487G>A		intron_variant		1	NM_152613.3	P1

Frequencies

GnomAD3 genomes AF: 0.292 AC: 44314 AN: 151942 Hom.: 6949 Cov.: 32

Gnomad AFR AF: 0.323

Gnomad AMI AF: 0.319

Gnomad AMR AF: 0.367

Gnomad ASJ AF: 0.371

Gnomad EAS AF: 0.0519

Gnomad SAS AF: 0.243

Gnomad FIN AF: 0.127

Gnomad MID AF: 0.280

Gnomad NFE AF: 0.299

Gnomad OTH AF: 0.297

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

GnomAD4 genome AF: 0.292 AC: 44344 AN: 152060 Hom.: 6957 Cov.: 32 AF XY: 0.282 AC XY: 20966 AN XY: 74350

Gnomad4 AFR AF: 0.323

Gnomad4 AMR AF: 0.367

Gnomad4 ASJ AF: 0.371

Gnomad4 EAS AF: 0.0508

Gnomad4 SAS AF: 0.243

Gnomad4 FIN AF: 0.127

Gnomad4 NFE AF: 0.299

Gnomad4 OTH AF: 0.294

Alfa AF: 0.304 Hom.: 6997

Bravo AF: 0.312

Asia WGS AF: 0.178 AC: 622 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.13
DANN	Benign	0.42

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: rs8138080; hg19: chr22-42396371;