10-102824573-C-T

Variant names:

• chr10-102824573-C-T
• rs4919682
• ENST00000647664.1:n.*300+2241C>T

Variant summary

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

The ENST00000647664.1(WBP1L):​n.*300+2241C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.235 in 151,974 control chromosomes in the GnomAD database, including 4,493 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 0.23 (4493 hom., cov: 32)
• Consequence: WBP1L ENST00000647664.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.97

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=-1.05).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.286 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
WBP1L	ENST00000647664.1	n.*300+2241C>T		intron_variant	Intron 5 of 7			ENSP00000498131.1

Frequencies

GnomAD3 genomes AF: 0.235 AC: 35675 AN: 151856 Hom.: 4494 Cov.: 32

Gnomad AFR AF: 0.153

Gnomad AMI AF: 0.180

Gnomad AMR AF: 0.249

Gnomad ASJ AF: 0.278

Gnomad EAS AF: 0.176

Gnomad SAS AF: 0.100

Gnomad FIN AF: 0.267

Gnomad MID AF: 0.228

Gnomad NFE AF: 0.289

Gnomad OTH AF: 0.231

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

GnomAD4 genome AF: 0.235 AC: 35679 AN: 151974 Hom.: 4493 Cov.: 32 AF XY: 0.232 AC XY: 17196 AN XY: 74278

Gnomad4 AFR AF: 0.153

Gnomad4 AMR AF: 0.249

Gnomad4 ASJ AF: 0.278

Gnomad4 EAS AF: 0.176

Gnomad4 SAS AF: 0.101

Gnomad4 FIN AF: 0.267

Gnomad4 NFE AF: 0.289

Gnomad4 OTH AF: 0.230

Alfa AF: 0.272 Hom.: 11710

Bravo AF: 0.232

Asia WGS AF: 0.125 AC: 434 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.98
DANN	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4919682; hg19: chr10-104584330;