13-41065289-TAAAAAAAAAAAAAA-TAAAAAAAAAAA

Variant names:

• chr13-41065289-TAAA-T
• rs58699334
• NM_007187.5:c.262+21_262+23delAAA

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The ENST00000379487.5(WBP4):​c.262+3_262+5delAAA variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0252 in 1,219,678 control chromosomes in the GnomAD database, with no homozygous occurrence. 1/1 splice prediction tools predict no significant impact on normal splicing. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.000073 (0 hom., cov: 25)
  • Exomes 𝑓: 0.027 (0 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 -8 ACMG points.

• BA1: GnomAdExome4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.0781 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
WBP4	NM_007187.5	c.262+21_262+23delAAA		intron_variant	Intron 4 of 9	ENST00000379487.5	NP_009118.1
WBP4	XM_005266245.3	c.355+21_355+23delAAA		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+5delAAA		splice_region_variant, intron_variant	Intron 4 of 9	1	NM_007187.5	ENSP00000368801.3

Frequencies

GnomAD3 genomes AF: 0.0000734 AC: 6 AN: 81774 Hom.: 0 Cov.: 25

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: 0.000615

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0000976

Gnomad OTH AF: 0.00

GnomAD3 exomes AF: 0.0995 AC: 3401 AN: 34198 Hom.: 0 AF XY: 0.101 AC XY: 1846 AN XY: 18256

Gnomad AFR exome AF: 0.0912

Gnomad AMR exome AF: 0.110

Gnomad ASJ exome AF: 0.0997

Gnomad EAS exome AF: 0.0940

Gnomad SAS exome AF: 0.0992

Gnomad FIN exome AF: 0.104

Gnomad NFE exome AF: 0.0988

Gnomad OTH exome AF: 0.0933

GnomAD4 exome AF: 0.0270 AC: 30698 AN: 1137876 Hom.: 0 AF XY: 0.0292 AC XY: 16218 AN XY: 554494

Gnomad4 AFR exome AF: 0.0385

Gnomad4 AMR exome AF: 0.0818

Gnomad4 ASJ exome AF: 0.0597

Gnomad4 EAS exome AF: 0.0697

Gnomad4 SAS exome AF: 0.0514

Gnomad4 FIN exome AF: 0.0695

Gnomad4 NFE exome AF: 0.0209

Gnomad4 OTH exome AF: 0.0376

GnomAD4 genome AF: 0.0000733 AC: 6 AN: 81802 Hom.: 0 Cov.: 25 AF XY: 0.0000784 AC XY: 3 AN XY: 38246

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: 0.000615

Gnomad4 NFE AF: 0.0000976

Gnomad4 OTH AF: 0.00

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;