10-102824573-C-T

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 26 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=-1.05).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.286 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

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

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	WBP1L	ENST00000647664.1		n.*300+2241C>T		intron	N/A	ENSP00000498131.1	A0A3B3IU90

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

African (AFR) AF: 0.153 AC: 6349 AN: 41476

American (AMR) AF: 0.249 AC: 3793 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.278 AC: 965 AN: 3472

East Asian (EAS) AF: 0.176 AC: 906 AN: 5162

South Asian (SAS) AF: 0.101 AC: 487 AN: 4812

European-Finnish (FIN) AF: 0.267 AC: 2814 AN: 10548

Middle Eastern (MID) AF: 0.231 AC: 68 AN: 294

European-Non Finnish (NFE) AF: 0.289 AC: 19650 AN: 67952

Other (OTH) AF: 0.230 AC: 483 AN: 2102

Alfa AF: 0.268 Hom.: 23790

Bravo AF: 0.232

Asia WGS AF: 0.125 AC: 434 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.98
DANN	Benign	0.59
PhyloP100		-2.0

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs4919682;

hg19: chr10-104584330;