chr13-41065289-TAA-T

Variant names:

• chr13-41065289-TAA-T
• rs58699334
• NM_007187.5:c.262+22_262+23delAA

Variant summary

Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP6 BA1

The ENST00000379487.5(WBP4):​c.262+3_262+4delAA variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0875 in 1,158,606 control chromosomes in the GnomAD database, including 6 homozygotes. 1/1 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in Lovd as Likely benign (no stars).

• Frequency:
  • Genomes: 𝑓 0.0082 (5 hom., cov: 25)
  • Exomes 𝑓: 0.094 (1 hom.)
• Consequence: WBP4 ENST00000379487.5 splice_region, intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.724

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]

ACMG classification

Verdict is Benign. Variant got -9 ACMG points.

• BP6: Variant 13-41065289-TAA-T is Benign according to our data. Variant chr13-41065289-TAA-T is described in Lovd as [Likely_benign].
• BA1: GnomAdExome4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.158 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
WBP4	NM_007187.5	c.262+22_262+23delAA		intron_variant	Intron 4 of 9	ENST00000379487.5	NP_009118.1
WBP4	XM_005266245.3	c.355+22_355+23delAA		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	c.262+3_262+4delAA		splice_region_variant, intron_variant	Intron 4 of 9	1	NM_007187.5	ENSP00000368801.3

Frequencies

GnomAD3 genomes AF: 0.00815 AC: 666 AN: 81764 Hom.: 5 Cov.: 25

Gnomad AFR AF: 0.0291

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00396

Gnomad ASJ AF: 0.000479

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000381

Gnomad FIN AF: 0.00185

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000293

Gnomad OTH AF: 0.00276

GnomAD3 exomes AF: 0.148 AC: 5078 AN: 34198 Hom.: 0 AF XY: 0.148 AC XY: 2702 AN XY: 18256

Gnomad AFR exome AF: 0.147

Gnomad AMR exome AF: 0.162

Gnomad ASJ exome AF: 0.158

Gnomad EAS exome AF: 0.142

Gnomad SAS exome AF: 0.170

Gnomad FIN exome AF: 0.131

Gnomad NFE exome AF: 0.140

Gnomad OTH exome AF: 0.161

GnomAD4 exome AF: 0.0936 AC: 100748 AN: 1076814 Hom.: 1 AF XY: 0.0965 AC XY: 50800 AN XY: 526334

Gnomad4 AFR exome AF: 0.118

Gnomad4 AMR exome AF: 0.156

Gnomad4 ASJ exome AF: 0.143

Gnomad4 EAS exome AF: 0.162

Gnomad4 SAS exome AF: 0.128

Gnomad4 FIN exome AF: 0.149

Gnomad4 NFE exome AF: 0.0844

Gnomad4 OTH exome AF: 0.108

GnomAD4 genome AF: 0.00817 AC: 668 AN: 81792 Hom.: 5 Cov.: 25 AF XY: 0.00805 AC XY: 308 AN XY: 38242

Gnomad4 AFR AF: 0.0291

Gnomad4 AMR AF: 0.00396

Gnomad4 ASJ AF: 0.000479

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.000381

Gnomad4 FIN AF: 0.00185

Gnomad4 NFE AF: 0.000293

Gnomad4 OTH AF: 0.00275

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs58699334; hg19: chr13-41639425;