rs6892

chr10-102816113-A-Gchr10-102816113-A-T

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The NM_001083913.2(WBP1L):c.*2782A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.15 in 152,600 control chromosomes in the GnomAD database, including 2,217 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 0.15 (2195 hom., cov: 32)
  • Exomes 𝑓: 0.28 (22 hom.)
• Consequence: WBP1L NM_001083913.2 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.384

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

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.43).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.214 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
WBP1L	NM_001083913.2	c.*2782A>G		3_prime_UTR_variant	4/4	ENST00000448841.7
WBP1L	NM_017787.5	c.*2782A>G		3_prime_UTR_variant	4/4
WBP1L	XM_011539913.3	c.*2782A>G		3_prime_UTR_variant	4/4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
WBP1L	ENST00000448841.7	c.*2782A>G		3_prime_UTR_variant	4/4	2	NM_001083913.2	A2
WBP1L	ENST00000369889.5	c.*2782A>G		3_prime_UTR_variant	4/4	1		P4
WBP1L	ENST00000647664.1	c.356-5104A>G		intron_variant, NMD_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.150 AC: 22764 AN: 152040 Hom.: 2188 Cov.: 32

Gnomad AFR AF: 0.0366

Gnomad AMI AF: 0.120

Gnomad AMR AF: 0.220

Gnomad ASJ AF: 0.140

Gnomad EAS AF: 0.149

Gnomad SAS AF: 0.209

Gnomad FIN AF: 0.299

Gnomad MID AF: 0.174

Gnomad NFE AF: 0.176

Gnomad OTH AF: 0.154

GnomAD4 exome AF: 0.278 AC: 123 AN: 442 Hom.: 22 Cov.: 0 AF XY: 0.319 AC XY: 83 AN XY: 260

Gnomad4 FIN exome AF: 0.280

Gnomad4 NFE exome AF: 0.500

Gnomad4 OTH exome AF: 0.125

GnomAD4 genome AF: 0.150 AC: 22776 AN: 152158 Hom.: 2195 Cov.: 32 AF XY: 0.157 AC XY: 11689 AN XY: 74382

Gnomad4 AFR AF: 0.0365

Gnomad4 AMR AF: 0.221

Gnomad4 ASJ AF: 0.140

Gnomad4 EAS AF: 0.149

Gnomad4 SAS AF: 0.210

Gnomad4 FIN AF: 0.299

Gnomad4 NFE AF: 0.176

Gnomad4 OTH AF: 0.153

Alfa AF: 0.154 Hom.: 278

Bravo AF: 0.140

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.43
Cadd	Benign	14
Dann	Benign	0.71
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.0

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs6892; hg19: chr10-104575870; COSMIC: COSV64009604;