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

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The ENST00000379487.5(WBP4):c.262+2_262+3insAAAAA variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000134 in 1,263,748 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.000037 ( 0 hom., cov: 25)

Exomes 𝑓: 0.00014 ( 0 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 Uncertain_significance. Variant got 2 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
WBP4	NM_007187.5 link	c.262+19_262+23dupAAAAA		intron_variant	Intron 4 of 9	ENST00000379487.5	NP_009118.1	O75554-1
WBP4	XM_005266245.3 link	c.355+19_355+23dupAAAAA		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+3insAAAAA		splice_region_variant, intron_variant	Intron 4 of 9	1	NM_007187.5	ENSP00000368801.3		O75554-1

Frequencies

GnomAD3 genomes

AF:

0.0000367

AC:

AN:

81784

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0000472

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.0000488

Gnomad OTH

AF:

0.00

GnomAD4 exome

AF:

0.000140

AC:

166

AN:

1181964

Hom.:

Cov.:

AF XY:

0.000156

AC XY:

AN XY:

576578

show subpopulations

Gnomad4 AFR exome

AF:

0.000118

Gnomad4 AMR exome

AF:

0.0000619

Gnomad4 ASJ exome

AF:

0.000236

Gnomad4 EAS exome

AF:

0.0000664

Gnomad4 SAS exome

AF:

0.000470

Gnomad4 FIN exome

AF:

0.000278

Gnomad4 NFE exome

AF:

0.000118

Gnomad4 OTH exome

AF:

0.000209

GnomAD4 genome

AF:

0.0000367

AC:

AN:

81784

Hom.:

Cov.:

AF XY:

0.0000523

AC XY:

AN XY:

38220

show subpopulations

Gnomad4 AFR

AF:

0.0000472

Gnomad4 AMR

AF:

0.00

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.0000488

Gnomad4 OTH

AF:

0.00

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