rs619824

Positions:

• chr10-102821531-A-C

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 0.499 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: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.391

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=-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/exons	MANE	Protein	UniProt
		n.102821531A>C		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
WBP1L	ENST00000647664.1	n.442+228A>C		intron_variant				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

Gnomad4 AFR AF: 0.342

Gnomad4 AMR AF: 0.551

Gnomad4 ASJ AF: 0.577

Gnomad4 EAS AF: 0.421

Gnomad4 SAS AF: 0.526

Gnomad4 FIN AF: 0.626

Gnomad4 NFE AF: 0.560

Gnomad4 OTH AF: 0.522

Alfa AF: 0.553 Hom.: 31583

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs619824; hg19: chr10-104581288;