Variant 13-41065289-TAAAAAAAAAAAAAA-TAAAAAAAAAAAAAAAAA details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The ENST00000379487.5(WBP4):c.262+2_262+3insAAA variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0483 in 1,198,040 control chromosomes in the GnomAD database, including 1,262 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.20 ( 1247 hom., cov: 25)

Exomes 𝑓: 0.037 ( 15 hom. )

Consequence

WBP4
ENST00000379487.5 splice_region, intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

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 -8 ACMG points.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.252 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
WBP4	NM_007187.5 link	c.262+21_262+23dupAAA		intron_variant	Intron 4 of 9	ENST00000379487.5	NP_009118.1	O75554-1
WBP4	XM_005266245.3 link	c.355+21_355+23dupAAA		intron_variant	Intron 4 of 9		XP_005266302.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
WBP4	ENST00000379487.5 link	c.262+2_262+3insAAA		splice_region_variant, intron_variant	Intron 4 of 9	1	NM_007187.5	ENSP00000368801.3		O75554-1

Frequencies

GnomAD3 genomes

AF:

0.202

AC:

16398

AN:

81294

Hom.:

1247

Cov.:

show subpopulations

Gnomad AFR

AF:

0.155

Gnomad AMI

AF:

0.186

Gnomad AMR

AF:

0.155

Gnomad ASJ

AF:

0.154

Gnomad EAS

AF:

0.0965

Gnomad SAS

AF:

0.104

Gnomad FIN

AF:

0.134

Gnomad MID

AF:

0.125

Gnomad NFE

AF:

0.256

Gnomad OTH

AF:

0.183

GnomAD3 exomes

AF:

0.0104

AC:

357

AN:

34198

Hom.:

AF XY:

0.0106

AC XY:

193

AN XY:

18256

show subpopulations

Gnomad AFR exome

AF:

0.0115

Gnomad AMR exome

AF:

0.00814

Gnomad ASJ exome

AF:

0.0116

Gnomad EAS exome

AF:

0.00686

Gnomad SAS exome

AF:

0.00938

Gnomad FIN exome

AF:

0.00282

Gnomad NFE exome

AF:

0.0129

Gnomad OTH exome

AF:

0.0157

GnomAD4 exome

AF:

0.0372

AC:

41521

AN:

1116718

Hom.:

Cov.:

AF XY:

0.0360

AC XY:

19682

AN XY:

546048

show subpopulations

Gnomad4 AFR exome

AF:

0.0193

Gnomad4 AMR exome

AF:

0.0104

Gnomad4 ASJ exome

AF:

0.0117

Gnomad4 EAS exome

AF:

0.00868

Gnomad4 SAS exome

AF:

0.0171

Gnomad4 FIN exome

AF:

0.0215

Gnomad4 NFE exome

AF:

0.0415

Gnomad4 OTH exome

AF:

0.0311

GnomAD4 genome

AF:

0.202

AC:

16397

AN:

81322

Hom.:

1247

Cov.:

AF XY:

0.194

AC XY:

7367

AN XY:

37978

show subpopulations

Gnomad4 AFR

AF:

0.155

Gnomad4 AMR

AF:

0.155

Gnomad4 ASJ

AF:

0.154

Gnomad4 EAS

AF:

0.0976

Gnomad4 SAS

AF:

0.104

Gnomad4 FIN

AF:

0.134

Gnomad4 NFE

AF:

0.256

Gnomad4 OTH

AF:

0.186

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over