13-41068626-CAGAAAGAAA-C

Variant names:

• chr13-41068626-CAGAAAGAAA-C
• rs534571354
• NM_007187.5:c.342_350delAGAAAAGAA

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM4 BS2

The NM_007187.5(WBP4):​c.342_350delAGAAAAGAA​(p.Glu115_Lys117del) variant causes a disruptive inframe deletion change. The variant allele was found at a frequency of 0.000507 in 1,612,986 control chromosomes in the GnomAD database, including 9 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.00041 (0 hom., cov: 32)
  • Exomes 𝑓: 0.00052 (9 hom.)
• Consequence: WBP4 NM_007187.5 disruptive_inframe_deletion
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 5.21

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 Likely_benign. Variant got -2 ACMG points.

• PM4: Nonframeshift variant in NON repetitive region in NM_007187.5.
• BS2: High Homozygotes in GnomAdExome4 at 9 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
WBP4	NM_007187.5	c.342_350delAGAAAAGAA	p.Glu115_Lys117del	disruptive_inframe_deletion	Exon 5 of 10	ENST00000379487.5	NP_009118.1
WBP4	XM_005266245.3	c.435_443delAGAAAAGAA	p.Glu146_Lys148del	disruptive_inframe_deletion	Exon 5 of 10		XP_005266302.1
WBP4	XM_047430071.1	c.-93_-85delAGAAAGAAA		upstream_gene_variant			XP_047286027.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
WBP4	ENST00000379487.5	c.342_350delAGAAAAGAA	p.Glu115_Lys117del	disruptive_inframe_deletion	Exon 5 of 10	1	NM_007187.5	ENSP00000368801.3

Frequencies

GnomAD3 genomes AF: 0.000415 AC: 63 AN: 151776 Hom.: 0 Cov.: 32

Gnomad AFR AF: 0.000363

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000328

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.000578

Gnomad SAS AF: 0.00752

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0000441

Gnomad OTH AF: 0.000479

GnomAD3 exomes AF: 0.000830 AC: 206 AN: 248260 Hom.: 3 AF XY: 0.00100 AC XY: 135 AN XY: 134450

Gnomad AFR exome AF: 0.000247

Gnomad AMR exome AF: 0.000203

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.000436

Gnomad SAS exome AF: 0.00589

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.0000541

Gnomad OTH exome AF: 0.000164

GnomAD4 exome AF: 0.000516 AC: 754 AN: 1461092 Hom.: 9 AF XY: 0.000655 AC XY: 476 AN XY: 726856

Gnomad4 AFR exome AF: 0.000568

Gnomad4 AMR exome AF: 0.000157

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.000227

Gnomad4 SAS exome AF: 0.00588

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.000163

Gnomad4 OTH exome AF: 0.000497

GnomAD4 genome AF: 0.000415 AC: 63 AN: 151894 Hom.: 0 Cov.: 32 AF XY: 0.000552 AC XY: 41 AN XY: 74238

Gnomad4 AFR AF: 0.000362

Gnomad4 AMR AF: 0.000327

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.000580

Gnomad4 SAS AF: 0.00753

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.0000441

Gnomad4 OTH AF: 0.000474

Alfa AF: 0.000174 Hom.: 0

Bravo AF: 0.000249

Asia WGS AF: 0.00433 AC: 15 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs534571354; hg19: chr13-41642762;