5-168431457-TCTGGCTGGCTGGCTGGCTGGCTGGCTGG-TCTGGCTGGCTGGCTGGCTGGCTGGCTGGCTGG

Position:

• chr5-168431457-TCTGGCTGGCTGGCTGGCTGGCTGGCTGG-TCTGGCTGGCTGGCTGGCTGGCTGGCTGGCTGG

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2

The NM_015238.3(WWC1):​c.2280+57_2280+60dupGCTG variant causes a intron change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.0021 (0 hom., cov: 0)
  • Exomes 𝑓: 0.0022 (8 hom.)
• Consequence: WWC1 NM_015238.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.765

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]

WWC1 (HGNC:):

ACMG classification

Verdict is Likely_benign. Variant got -4 ACMG points.

• BS2: High Homozygotes in GnomAdExome4 at 8 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
WWC1	NM_015238.3	c.2280+57_2280+60dupGCTG		intron_variant		ENST00000265293.9	NP_056053.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
WWC1	ENST00000265293.9	c.2280+57_2280+60dupGCTG		intron_variant		1	NM_015238.3	ENSP00000265293.4

Frequencies

GnomAD3 genomes AF: 0.00208 AC: 309 AN: 148352 Hom.: 0 Cov.: 0

Gnomad AFR AF: 0.000921

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00283

Gnomad ASJ AF: 0.0242

Gnomad EAS AF: 0.00120

Gnomad SAS AF: 0.00339

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00182

Gnomad OTH AF: 0.00200

GnomAD3 exomes AF: 0.00246 AC: 311 AN: 126504 Hom.: 0 AF XY: 0.00262 AC XY: 178 AN XY: 68006

Gnomad AFR exome AF: 0.000983

Gnomad AMR exome AF: 0.00169

Gnomad ASJ exome AF: 0.0227

Gnomad EAS exome AF: 0.00172

Gnomad SAS exome AF: 0.00352

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.00178

Gnomad OTH exome AF: 0.00274

GnomAD4 exome AF: 0.00219 AC: 2778 AN: 1266008 Hom.: 8 Cov.: 0 AF XY: 0.00229 AC XY: 1439 AN XY: 628320

Gnomad4 AFR exome AF: 0.00101

Gnomad4 AMR exome AF: 0.00133

Gnomad4 ASJ exome AF: 0.0286

Gnomad4 EAS exome AF: 0.00186

Gnomad4 SAS exome AF: 0.00371

Gnomad4 FIN exome AF: 0.000393

Gnomad4 NFE exome AF: 0.00158

Gnomad4 OTH exome AF: 0.00388

GnomAD4 genome AF: 0.00207 AC: 308 AN: 148462 Hom.: 0 Cov.: 0 AF XY: 0.00194 AC XY: 140 AN XY: 72194

Gnomad4 AFR AF: 0.000894

Gnomad4 AMR AF: 0.00282

Gnomad4 ASJ AF: 0.0242

Gnomad4 EAS AF: 0.00121

Gnomad4 SAS AF: 0.00339

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.00182

Gnomad4 OTH AF: 0.00198

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;