ENST00000647664.1:n.*417+535G>T

Variant names:

• chr10-102827605-G-T
• rs4919685
• ENST00000647664.1:n.*417+535G>T

Variant summary

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

The ENST00000647664.1(WBP1L):​n.*417+535G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.241 in 152,120 control chromosomes in the GnomAD database, including 4,733 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 0.24 (4733 hom., cov: 31)
• Consequence: WBP1L ENST00000647664.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.149
• Publications: 17 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=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.296 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.*417+535G>T		intron	N/A	ENSP00000498131.1

Frequencies

GnomAD3 genomes AF: 0.241 AC: 36626 AN: 152002 Hom.: 4733 Cov.: 31

Gnomad AFR AF: 0.164

Gnomad AMI AF: 0.180

Gnomad AMR AF: 0.229

Gnomad ASJ AF: 0.306

Gnomad EAS AF: 0.158

Gnomad SAS AF: 0.104

Gnomad FIN AF: 0.269

Gnomad MID AF: 0.275

Gnomad NFE AF: 0.299

Gnomad OTH AF: 0.242

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

GnomAD4 genome AF: 0.241 AC: 36627 AN: 152120 Hom.: 4733 Cov.: 31 AF XY: 0.236 AC XY: 17579 AN XY: 74354

African (AFR) AF: 0.164 AC: 6812 AN: 41516

American (AMR) AF: 0.228 AC: 3489 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.306 AC: 1063 AN: 3470

East Asian (EAS) AF: 0.158 AC: 815 AN: 5170

South Asian (SAS) AF: 0.105 AC: 508 AN: 4826

European-Finnish (FIN) AF: 0.269 AC: 2843 AN: 10560

Middle Eastern (MID) AF: 0.282 AC: 83 AN: 294

European-Non Finnish (NFE) AF: 0.299 AC: 20342 AN: 67976

Other (OTH) AF: 0.241 AC: 508 AN: 2112

Alfa AF: 0.272 Hom.: 7314

Bravo AF: 0.236

Asia WGS AF: 0.124 AC: 430 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.68
DANN	Benign	0.68
PhyloP100		-0.15

Splicing

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

Other links and lift over

dbSNP: rs4919685; hg19: chr10-104587362;