5-168431457-TCTGGCTGGCTGGCTGGCTGGCTGGCTGG-TCTGGCTGGCTGGCTGGCTGG

Variant summary

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

The NM_015238.3(WWC1):c.2280+53_2280+60del variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.485 in 1,391,104 control chromosomes in the GnomAD database, including 162,812 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.53 (21480 hom., cov: 0)
  • Exomes 𝑓: 0.48 (141332 hom.)
• Consequence: WWC1 NM_015238.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.31

Genes affected

WWC1 (HGNC:29435): (WW and C2 domain containing 1) The protein encoded by this gene is a cytoplasmic phosphoprotein that interacts with PRKC-zeta and dynein light chain-1. Alleles of this gene have been found that enhance memory in some individuals. Three transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Mar 2010]

ACMG classification

Verdict is Benign. Variant got -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.714 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
WWC1	NM_015238.3	c.2280+53_2280+60del		intron_variant		ENST00000265293.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
WWC1	ENST00000265293.9	c.2280+53_2280+60del		intron_variant		1	NM_015238.3	P1

Frequencies

GnomAD3 genomes AF: 0.534 AC: 79032 AN: 148112 Hom.: 21457 Cov.: 0

Gnomad AFR AF: 0.604

Gnomad AMI AF: 0.613

Gnomad AMR AF: 0.560

Gnomad ASJ AF: 0.513

Gnomad EAS AF: 0.734

Gnomad SAS AF: 0.552

Gnomad FIN AF: 0.472

Gnomad MID AF: 0.417

Gnomad NFE AF: 0.480

Gnomad OTH AF: 0.503

GnomAD3 exomes AF: 0.535 AC: 67723 AN: 126504 Hom.: 18435 AF XY: 0.533 AC XY: 36266 AN XY: 68006

Gnomad AFR exome AF: 0.549

Gnomad AMR exome AF: 0.633

Gnomad ASJ exome AF: 0.517

Gnomad EAS exome AF: 0.716

Gnomad SAS exome AF: 0.556

Gnomad FIN exome AF: 0.479

Gnomad NFE exome AF: 0.470

Gnomad OTH exome AF: 0.499

GnomAD4 exome AF: 0.479 AC: 595789 AN: 1242884 Hom.: 141332 AF XY: 0.480 AC XY: 295899 AN XY: 616098

Gnomad4 AFR exome AF: 0.552

Gnomad4 AMR exome AF: 0.592

Gnomad4 ASJ exome AF: 0.476

Gnomad4 EAS exome AF: 0.653

Gnomad4 SAS exome AF: 0.518

Gnomad4 FIN exome AF: 0.464

Gnomad4 NFE exome AF: 0.465

Gnomad4 OTH exome AF: 0.487

GnomAD4 genome AF: 0.534 AC: 79091 AN: 148220 Hom.: 21480 Cov.: 0 AF XY: 0.538 AC XY: 38787 AN XY: 72060

Gnomad4 AFR AF: 0.604

Gnomad4 AMR AF: 0.560

Gnomad4 ASJ AF: 0.513

Gnomad4 EAS AF: 0.734

Gnomad4 SAS AF: 0.551

Gnomad4 FIN AF: 0.472

Gnomad4 NFE AF: 0.480

Gnomad4 OTH AF: 0.503

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: rs11279828; hg19: chr5-167858462;