rs11191401

Variant names:

• chr10-102813646-A-G
• rs11191401
• NM_001083913.2:c.*315A>G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001083913.2(WBP1L):​c.*315A>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 0.254 in 364,742 control chromosomes in the GnomAD database, including 12,825 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 (4688 hom., cov: 32)
  • Exomes 𝑓: 0.26 (8137 hom.)
• Consequence: WBP1L NM_001083913.2 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0470

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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.291 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
WBP1L	NM_001083913.2	c.*315A>G		3_prime_UTR_variant	Exon 4 of 4	ENST00000448841.7	NP_001077382.1
WBP1L	NM_017787.5	c.*315A>G		3_prime_UTR_variant	Exon 4 of 4		NP_060257.4
WBP1L	XM_011539913.3	c.*315A>G		3_prime_UTR_variant	Exon 4 of 4		XP_011538215.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
WBP1L	ENST00000448841.7	c.*315A>G		3_prime_UTR_variant	Exon 4 of 4	2	NM_001083913.2	ENSP00000414721.1
WBP1L	ENST00000369889.5	c.*315A>G		3_prime_UTR_variant	Exon 4 of 4	1		ENSP00000358905.4
WBP1L	ENST00000647664.1	n.355+3592A>G		intron_variant	Intron 3 of 7			ENSP00000498131.1

Frequencies

GnomAD3 genomes AF: 0.242 AC: 36719 AN: 151926 Hom.: 4688 Cov.: 32

Gnomad AFR AF: 0.169

Gnomad AMI AF: 0.182

Gnomad AMR AF: 0.250

Gnomad ASJ AF: 0.279

Gnomad EAS AF: 0.166

Gnomad SAS AF: 0.106

Gnomad FIN AF: 0.264

Gnomad MID AF: 0.260

Gnomad NFE AF: 0.294

Gnomad OTH AF: 0.244

GnomAD4 exome AF: 0.264 AC: 56054 AN: 212696 Hom.: 8137 Cov.: 2 AF XY: 0.259 AC XY: 28507 AN XY: 109916

Gnomad4 AFR exome AF: 0.162

Gnomad4 AMR exome AF: 0.243

Gnomad4 ASJ exome AF: 0.272

Gnomad4 EAS exome AF: 0.108

Gnomad4 SAS exome AF: 0.113

Gnomad4 FIN exome AF: 0.293

Gnomad4 NFE exome AF: 0.302

Gnomad4 OTH exome AF: 0.273

GnomAD4 genome AF: 0.242 AC: 36722 AN: 152046 Hom.: 4688 Cov.: 32 AF XY: 0.237 AC XY: 17636 AN XY: 74324

Gnomad4 AFR AF: 0.169

Gnomad4 AMR AF: 0.250

Gnomad4 ASJ AF: 0.279

Gnomad4 EAS AF: 0.166

Gnomad4 SAS AF: 0.107

Gnomad4 FIN AF: 0.264

Gnomad4 NFE AF: 0.294

Gnomad4 OTH AF: 0.243

Alfa AF: 0.281 Hom.: 4645

Bravo AF: 0.240

Asia WGS AF: 0.123 AC: 426 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	8.0
DANN	Benign	0.78

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: rs11191401; hg19: chr10-104573403;