rs10883782

Variant names:

• chr10-102824175-A-G
• rs10883782
• ENST00000647664.1:n.*300+1843A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000647664.1(WBP1L):​n.*300+1843A>G variant causes a intron 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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.359
• Publications: 13 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000647664.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	WBP1L	ENST00000647664.1		n.*300+1843A>G		intron	N/A	ENSP00000498131.1

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

African (AFR) AF: 0.108 AC: 4497 AN: 41522

American (AMR) AF: 0.137 AC: 2098 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.240 AC: 830 AN: 3464

East Asian (EAS) AF: 0.151 AC: 780 AN: 5178

South Asian (SAS) AF: 0.163 AC: 784 AN: 4824

European-Finnish (FIN) AF: 0.0736 AC: 780 AN: 10602

Middle Eastern (MID) AF: 0.255 AC: 75 AN: 294

European-Non Finnish (NFE) AF: 0.161 AC: 10929 AN: 67988

Other (OTH) AF: 0.173 AC: 365 AN: 2106

Alfa AF: 0.163 Hom.: 3772

Bravo AF: 0.146

Asia WGS AF: 0.151 AC: 526 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.40
DANN	Benign	0.62
PhyloP100		-0.36

Splicing

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

Other links and lift over

dbSNP: rs10883782; hg19: chr10-104583932;