10-102814099-C-T

Variant names:

• chr10-102814099-C-T
• rs17115073
• NM_001083913.2:c.*768C>T

Variant summary

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

The NM_001083913.2(WBP1L):​c.*768C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0496 in 152,264 control chromosomes in the GnomAD database, including 417 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 0.050 (417 hom., cov: 33)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: WBP1L NM_001083913.2 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0250
• Publications: 3 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 (AFR) allele frequency at 95% confidence interval = 0.122 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
WBP1L	NM_001083913.2	c.*768C>T		3_prime_UTR_variant	Exon 4 of 4	ENST00000448841.7	NP_001077382.1
WBP1L	NM_017787.5	c.*768C>T		3_prime_UTR_variant	Exon 4 of 4		NP_060257.4
WBP1L	XM_011539913.3	c.*768C>T		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.*768C>T		3_prime_UTR_variant	Exon 4 of 4	2	NM_001083913.2	ENSP00000414721.1
WBP1L	ENST00000369889.5	c.*768C>T		3_prime_UTR_variant	Exon 4 of 4	1		ENSP00000358905.4
WBP1L	ENST00000647664.1	n.355+4045C>T		intron_variant	Intron 3 of 7			ENSP00000498131.1

Frequencies

GnomAD3 genomes AF: 0.0497 AC: 7555 AN: 152146 Hom.: 417 Cov.: 33

Gnomad AFR AF: 0.125

Gnomad AMI AF: 0.00440

Gnomad AMR AF: 0.0221

Gnomad ASJ AF: 0.0510

Gnomad EAS AF: 0.00269

Gnomad SAS AF: 0.113

Gnomad FIN AF: 0.00376

Gnomad MID AF: 0.0475

Gnomad NFE AF: 0.0172

Gnomad OTH AF: 0.0449

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 6 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 4

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 6

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AC: 0 AN: 0

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.0496 AC: 7553 AN: 152264 Hom.: 417 Cov.: 33 AF XY: 0.0484 AC XY: 3608 AN XY: 74474

African (AFR) AF: 0.124 AC: 5168 AN: 41530

American (AMR) AF: 0.0219 AC: 335 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.0510 AC: 177 AN: 3470

East Asian (EAS) AF: 0.00251 AC: 13 AN: 5186

South Asian (SAS) AF: 0.112 AC: 538 AN: 4814

European-Finnish (FIN) AF: 0.00376 AC: 40 AN: 10626

Middle Eastern (MID) AF: 0.0442 AC: 13 AN: 294

European-Non Finnish (NFE) AF: 0.0172 AC: 1171 AN: 68020

Other (OTH) AF: 0.0444 AC: 94 AN: 2116

Alfa AF: 0.0189 Hom.: 17

Bravo AF: 0.0515

Asia WGS AF: 0.0640 AC: 220 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	0.52
PhyloP100		-0.025
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: rs17115073; hg19: chr10-104573856;