Variant chr13-41065289-TA-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP6BA1

The NM_007187.5(WBP4):c.262+23del variant causes a splice donor region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.211 in 1,233,398 control chromosomes in the GnomAD database, including 10 homozygotes. Variant has been reported in ClinVar as Likely benign (no stars).

Frequency

Genomes: 𝑓 0.0046 ( 2 hom., cov: 25)

Exomes 𝑓: 0.23 ( 8 hom. )

Consequence

WBP4
NM_007187.5 splice_donor_region, intron

Scores

Not classified

Clinical Significance

Benign/Likely benign no assertion criteria provided B:2

Conservation

PhyloP100: 0.0850

Variant links:

Genes affected

WBP4 (HGNC:12739): (WW domain binding protein 4) This gene encodes WW domain-containing binding protein 4. The WW domain represents a small and compact globular structure that interacts with proline-rich ligands. This encoded protein is a general spliceosomal protein that may play a role in cross-intron bridging of U1 and U2 snRNPs in the spliceosomal complex A. [provided by RefSeq, Jul 2008]

WBP4 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -9 ACMG points.

BP6

Variant 13-41065289-TA-T is Benign according to our data. Variant chr13-41065289-TA-T is described in ClinVar as [Likely_benign]. Clinvar id is 1285194.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr13-41065289-TA-T is described in Lovd as [Benign]. Variant chr13-41065289-TA-T is described in Lovd as [Likely_benign].

BA1

GnomAdExome4 highest subpopulation (MID) allele frequency at 95% confidence interval = 0.23 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
WBP4	NM_007187.5 linkuse as main transcript	c.262+23del		splice_donor_region_variant, intron_variant		ENST00000379487.5
WBP4	XM_005266245.3 linkuse as main transcript	c.355+23del		splice_donor_region_variant, intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
WBP4	ENST00000379487.5 linkuse as main transcript	c.262+23del		splice_donor_region_variant, intron_variant		1	NM_007187.5	P1	O75554-1

Frequencies

GnomAD3 genomes

AF:

0.00459

AC:

375

AN:

81782

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0117

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00509

Gnomad ASJ

AF:

0.000479

Gnomad EAS

AF:

0.00177

Gnomad SAS

AF:

0.00190

Gnomad FIN

AF:

0.00461

Gnomad MID

AF:

0.00893

Gnomad NFE

AF:

0.00144

Gnomad OTH

AF:

0.00460

GnomAD3 exomes

AF:

0.137

AC:

4698

AN:

34198

Hom.:

AF XY:

0.135

AC XY:

2460

AN XY:

18256

show subpopulations

Gnomad AFR exome

AF:

0.141

Gnomad AMR exome

AF:

0.163

Gnomad ASJ exome

AF:

0.136

Gnomad EAS exome

AF:

0.161

Gnomad SAS exome

AF:

0.139

Gnomad FIN exome

AF:

0.112

Gnomad NFE exome

AF:

0.122

Gnomad OTH exome

AF:

0.161

GnomAD4 exome

AF:

0.226

AC:

260322

AN:

1151588

Hom.:

Cov.:

AF XY:

0.224

AC XY:

125896

AN XY:

561996

show subpopulations

Gnomad4 AFR exome

AF:

0.230

Gnomad4 AMR exome

AF:

0.172

Gnomad4 ASJ exome

AF:

0.215

Gnomad4 EAS exome

AF:

0.199

Gnomad4 SAS exome

AF:

0.191

Gnomad4 FIN exome

AF:

0.184

Gnomad4 NFE exome

AF:

0.231

Gnomad4 OTH exome

AF:

0.225

GnomAD4 genome

AF:

0.00461

AC:

377

AN:

81810

Hom.:

Cov.:

AF XY:

0.00484

AC XY:

185

AN XY:

38250

show subpopulations

Gnomad4 AFR

AF:

0.0117

Gnomad4 AMR

AF:

0.00523

Gnomad4 ASJ

AF:

0.000479

Gnomad4 EAS

AF:

0.00178

Gnomad4 SAS

AF:

0.00191

Gnomad4 FIN

AF:

0.00461

Gnomad4 NFE

AF:

0.00144

Gnomad4 OTH

AF:

0.00549

ClinVar

Significance: Benign/Likely benign

Submissions summary: Benign:2

Revision: no assertion criteria provided

LINK: link

Submissions by phenotype

not specified

Benign:1

Benign, no assertion criteria provided

clinical testing

Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center

- -

not provided

Benign:1

Likely benign, no assertion criteria provided

clinical testing

Genome Diagnostics Laboratory, University Medical Center Utrecht

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over