10-102824573-C-T

Position:

• chr10-102824573-C-T

Variant summary

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

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: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.97

Genes affected

(HGNC:):

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/exons	MANE	Protein	UniProt
		n.102824573C>T		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
WBP1L	ENST00000647664.1	n.*300+2241C>T		intron_variant				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;