rs10883782

chr10-102824175-A-G

Variant summary

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

The ENST00000647664.1(WBP1L):c.*300+1843A>G variant causes a intron, NMD transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.141 in 152,168 control chromosomes in the GnomAD database, including 1,640 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 0.14 (1640 hom., cov: 32)
• Consequence: WBP1L ENST00000647664.1 intron, NMD_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.359

Genes affected

WBP1L (HGNC:23510): (WW domain binding protein 1 like) Predicted to enable ubiquitin protein ligase binding activity. Predicted to act upstream of or within CXCL12-activated CXCR4 signaling pathway; hemopoiesis; and positive regulation of protein ubiquitination. Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.158 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
WBP1L	ENST00000647664.1	c.*300+1843A>G		intron_variant, NMD_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.141 AC: 21498 AN: 152050 Hom.: 1641 Cov.: 32

Gnomad AFR AF: 0.108

Gnomad AMI AF: 0.400

Gnomad AMR AF: 0.137

Gnomad ASJ AF: 0.240

Gnomad EAS AF: 0.151

Gnomad SAS AF: 0.163

Gnomad FIN AF: 0.0736

Gnomad MID AF: 0.269

Gnomad NFE AF: 0.161

Gnomad OTH AF: 0.172

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

GnomAD4 genome AF: 0.141 AC: 21501 AN: 152168 Hom.: 1640 Cov.: 32 AF XY: 0.137 AC XY: 10227 AN XY: 74410

Gnomad4 AFR AF: 0.108

Gnomad4 AMR AF: 0.137

Gnomad4 ASJ AF: 0.240

Gnomad4 EAS AF: 0.151

Gnomad4 SAS AF: 0.163

Gnomad4 FIN AF: 0.0736

Gnomad4 NFE AF: 0.161

Gnomad4 OTH AF: 0.173

Alfa AF: 0.165 Hom.: 3063

Bravo AF: 0.146

Asia WGS AF: 0.151 AC: 526 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	0.40
Dann	Benign	0.62

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs10883782; hg19: chr10-104583932;