rs11191401

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 21 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=-0.77).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.291 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001083913.2. 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
	WBP1L	NM_001083913.2	MANE Select	c.*315A>G		3_prime_UTR	Exon 4 of 4	NP_001077382.1
	WBP1L	NM_017787.5		c.*315A>G		3_prime_UTR	Exon 4 of 4	NP_060257.4

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	WBP1L	ENST00000448841.7	TSL:2 MANE Select	c.*315A>G		3_prime_UTR	Exon 4 of 4	ENSP00000414721.1
	WBP1L	ENST00000369889.5	TSL:1	c.*315A>G		3_prime_UTR	Exon 4 of 4	ENSP00000358905.4
	WBP1L	ENST00000647664.1		n.355+3592A>G		intron	N/A	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

African (AFR) AF: 0.162 AC: 1140 AN: 7052

American (AMR) AF: 0.243 AC: 1977 AN: 8136

Ashkenazi Jewish (ASJ) AF: 0.272 AC: 1977 AN: 7280

East Asian (EAS) AF: 0.108 AC: 1723 AN: 15892

South Asian (SAS) AF: 0.113 AC: 1697 AN: 15066

European-Finnish (FIN) AF: 0.293 AC: 3833 AN: 13070

Middle Eastern (MID) AF: 0.284 AC: 300 AN: 1056

European-Non Finnish (NFE) AF: 0.302 AC: 39786 AN: 131892

Other (OTH) AF: 0.273 AC: 3621 AN: 13252

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

African (AFR) AF: 0.169 AC: 7010 AN: 41486

American (AMR) AF: 0.250 AC: 3817 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.279 AC: 969 AN: 3468

East Asian (EAS) AF: 0.166 AC: 859 AN: 5184

South Asian (SAS) AF: 0.107 AC: 515 AN: 4816

European-Finnish (FIN) AF: 0.264 AC: 2785 AN: 10556

Middle Eastern (MID) AF: 0.264 AC: 77 AN: 292

European-Non Finnish (NFE) AF: 0.294 AC: 20011 AN: 67954

Other (OTH) AF: 0.243 AC: 513 AN: 2112

Alfa AF: 0.281 Hom.: 5404

Bravo AF: 0.240

Asia WGS AF: 0.123 AC: 426 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	8.0
DANN	Benign	0.78
PhyloP100		0.047
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs11191401; hg19: chr10-104573403;