13-41065289-TAAAAAAAAAAAAAA-TAAAAAAAAAAAAAAAAAAAAAA

Variant summary

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

The ENST00000379487.5(WBP4):​c.262+2_262+3insAAAAAAAA variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000712 in 1,263,960 control chromosomes in the GnomAD database, including 1 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.000024 ( 1 hom., cov: 25)
Exomes 𝑓: 0.0000059 ( 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]

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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
WBP4NM_007187.5 linkc.262+16_262+23dupAAAAAAAA intron_variant Intron 4 of 9 ENST00000379487.5 NP_009118.1 O75554-1
WBP4XM_005266245.3 linkc.355+16_355+23dupAAAAAAAA intron_variant Intron 4 of 9 XP_005266302.1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
WBP4ENST00000379487.5 linkc.262+2_262+3insAAAAAAAA splice_region_variant, intron_variant Intron 4 of 9 1 NM_007187.5 ENSP00000368801.3 O75554-1

Frequencies

GnomAD3 genomes
AF:
0.0000245
AC:
2
AN:
81788
Hom.:
1
Cov.:
25
show subpopulations
Gnomad AFR
AF:
0.00
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:
0.00000592
AC:
7
AN:
1182172
Hom.:
0
Cov.:
0
AF XY:
0.00000694
AC XY:
4
AN XY:
576650
show subpopulations
Gnomad4 AFR exome
AF:
0.0000395
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.0000188
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00000519
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
AF:
0.0000245
AC:
2
AN:
81788
Hom.:
1
Cov.:
25
AF XY:
0.0000523
AC XY:
2
AN XY:
38220
show subpopulations
Gnomad4 AFR
AF:
0.00
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.

Other links and lift over

dbSNP: rs58699334; hg19: chr13-41639425; API