rs619824

Variant names:

• chr10-102821531-A-C
• rs619824
• ENST00000647664.1:n.442+228A>C

Variant summary

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

The ENST00000647664.1(WBP1L):​n.442+228A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.499 in 152,046 control chromosomes in the GnomAD database, including 19,692 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 0.50 (19692 hom., cov: 32)
• Consequence: WBP1L ENST00000647664.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.391
• Publications: 39 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=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.555 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.442+228A>C		intron_variant	Intron 4 of 7			ENSP00000498131.1

Frequencies

GnomAD3 genomes AF: 0.499 AC: 75849 AN: 151928 Hom.: 19693 Cov.: 32

Gnomad AFR AF: 0.342

Gnomad AMI AF: 0.693

Gnomad AMR AF: 0.551

Gnomad ASJ AF: 0.577

Gnomad EAS AF: 0.420

Gnomad SAS AF: 0.526

Gnomad FIN AF: 0.626

Gnomad MID AF: 0.595

Gnomad NFE AF: 0.560

Gnomad OTH AF: 0.524

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

GnomAD4 genome AF: 0.499 AC: 75874 AN: 152046 Hom.: 19692 Cov.: 32 AF XY: 0.505 AC XY: 37509 AN XY: 74322

African (AFR) AF: 0.342 AC: 14179 AN: 41480

American (AMR) AF: 0.551 AC: 8419 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.577 AC: 2001 AN: 3468

East Asian (EAS) AF: 0.421 AC: 2169 AN: 5158

South Asian (SAS) AF: 0.526 AC: 2534 AN: 4818

European-Finnish (FIN) AF: 0.626 AC: 6611 AN: 10560

Middle Eastern (MID) AF: 0.588 AC: 173 AN: 294

European-Non Finnish (NFE) AF: 0.560 AC: 38053 AN: 67970

Other (OTH) AF: 0.522 AC: 1103 AN: 2112

Alfa AF: 0.550 Hom.: 36163

Bravo AF: 0.489

Asia WGS AF: 0.499 AC: 1742 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.12
DANN	Benign	0.50
PhyloP100		-0.39

Splicing

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

Other links and lift over

dbSNP: rs619824; hg19: chr10-104581288;