13-41065289-TAAAAAAAAAAAAAA-TAAAAAAAAAAAAAAAAAAAA
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The ENST00000379487.5(WBP4):c.262+2_262+3insAAAAAA variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000491 in 1,263,956 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 0.000049 ( 0 hom., cov: 25)
Exomes 𝑓: 0.000049 ( 0 hom. )
Consequence
WBP4
ENST00000379487.5 splice_region, intron
ENST00000379487.5 splice_region, intron
Scores
Not classified
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.0850
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]
Genome browser will be placed here
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
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000489 AC: 4AN: 81780Hom.: 0 Cov.: 25
GnomAD3 genomes
AF:
AC:
4
AN:
81780
Hom.:
Cov.:
25
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD4 exome AF: 0.0000491 AC: 58AN: 1182148Hom.: 0 Cov.: 0 AF XY: 0.0000659 AC XY: 38AN XY: 576644
GnomAD4 exome
AF:
AC:
58
AN:
1182148
Hom.:
Cov.:
0
AF XY:
AC XY:
38
AN XY:
576644
Gnomad4 AFR exome
AF:
Gnomad4 AMR exome
AF:
Gnomad4 ASJ exome
AF:
Gnomad4 EAS exome
AF:
Gnomad4 SAS exome
AF:
Gnomad4 FIN exome
AF:
Gnomad4 NFE exome
AF:
Gnomad4 OTH exome
AF:
GnomAD4 genome AF: 0.0000489 AC: 4AN: 81808Hom.: 0 Cov.: 25 AF XY: 0.0000784 AC XY: 3AN XY: 38250
GnomAD4 genome
AF:
AC:
4
AN:
81808
Hom.:
Cov.:
25
AF XY:
AC XY:
3
AN XY:
38250
Gnomad4 AFR
AF:
Gnomad4 AMR
AF:
Gnomad4 ASJ
AF:
Gnomad4 EAS
AF:
Gnomad4 SAS
AF:
Gnomad4 FIN
AF:
Gnomad4 NFE
AF:
Gnomad4 OTH
AF:
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at