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

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2

The ENST00000379487.5(WBP4):c.262+2_262+3insAAAA variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00152 in 1,260,258 control chromosomes in the GnomAD database, including 3 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.0024 ( 1 hom., cov: 25)

Exomes 𝑓: 0.0015 ( 2 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 Likely_benign. Variant got -4 ACMG points.

BS2

High Homozygotes in GnomAdExome4 at 2 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
WBP4	NM_007187.5 link	c.262+20_262+23dupAAAA		intron_variant	Intron 4 of 9	ENST00000379487.5	NP_009118.1	O75554-1
WBP4	XM_005266245.3 link	c.355+20_355+23dupAAAA		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+3insAAAA		splice_region_variant, intron_variant	Intron 4 of 9	1	NM_007187.5	ENSP00000368801.3		O75554-1

Frequencies

GnomAD3 genomes

AF:

0.00242

AC:

198

AN:

81718

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00543

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00184

Gnomad ASJ

AF:

0.000479

Gnomad EAS

AF:

0.00283

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.000308

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00137

Gnomad OTH

AF:

0.00368

GnomAD4 exome

AF:

0.00146

AC:

1718

AN:

1178512

Hom.:

Cov.:

AF XY:

0.00151

AC XY:

870

AN XY:

575008

show subpopulations

Gnomad4 AFR exome

AF:

0.00150

Gnomad4 AMR exome

AF:

0.00143

Gnomad4 ASJ exome

AF:

0.00100

Gnomad4 EAS exome

AF:

0.000697

Gnomad4 SAS exome

AF:

0.00273

Gnomad4 FIN exome

AF:

0.00266

Gnomad4 NFE exome

AF:

0.00139

Gnomad4 OTH exome

AF:

0.00147

GnomAD4 genome

AF:

0.00242

AC:

198

AN:

81746

Hom.:

Cov.:

AF XY:

0.00254

AC XY:

AN XY:

38216

show subpopulations

Gnomad4 AFR

AF:

0.00542

Gnomad4 AMR

AF:

0.00184

Gnomad4 ASJ

AF:

0.000479

Gnomad4 EAS

AF:

0.00284

Gnomad4 SAS

AF:

0.00

Gnomad4 FIN

AF:

0.000308

Gnomad4 NFE

AF:

0.00137

Gnomad4 OTH

AF:

0.00366

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