chr22-42020691-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

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

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0450
Variant links:
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]

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ACMG classification

Classification made for transcript

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
WBP2NLNM_152613.3 linkuse as main transcriptc.406+595G>T intron_variant ENST00000328823.13

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
WBP2NLENST00000328823.13 linkuse as main transcriptc.406+595G>T intron_variant 1 NM_152613.3 P1

Frequencies

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

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs133337; hg19: chr22-42416695; API