NM_015238.3:c.2280+49_2280+60dupGCTGGCTGGCTG

Variant names:

• chr5-168431457-T-TCTGGCTGGCTGG
• rs11279828
• NM_015238.3:c.2280+49_2280+60dupGCTGGCTGGCTG

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.

The NM_015238.3(WWC1):​c.2280+49_2280+60dupGCTGGCTGGCTG variant causes a intron change involving the alteration of a non-conserved nucleotide. It is difficult to determine the true allele frequency of this variant because it is of type INS_BIG, and the frequency of such variant types in population databases may be underestimated and unreliable. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.000054 (0 hom., cov: 0)
  • Exomes 𝑓: 0.000063 (0 hom.)
• Consequence: WWC1 NM_015238.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.765
• Publications: 2 publications found

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

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
WWC1	NM_015238.3	c.2280+49_2280+60dupGCTGGCTGGCTG		intron_variant	Intron 15 of 22	ENST00000265293.9	NP_056053.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
WWC1	ENST00000265293.9	c.2280+13_2280+14insCTGGCTGGCTGG		intron_variant	Intron 15 of 22	1	NM_015238.3	ENSP00000265293.4

Frequencies

GnomAD3 genomes AF: 0.0000539 AC: 8 AN: 148354 Hom.: 0 Cov.: 0

Gnomad AFR AF: 0.0000996

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0000673

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0000149

Gnomad OTH AF: 0.000999

GnomAD4 exome AF: 0.0000632 AC: 80 AN: 1266096 Hom.: 0 Cov.: 0 AF XY: 0.0000812 AC XY: 51 AN XY: 628358

African (AFR) AF: 0.000104 AC: 3 AN: 28758

American (AMR) AF: 0.000186 AC: 6 AN: 32320

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 20524

East Asian (EAS) AF: 0.0000831 AC: 3 AN: 36082

South Asian (SAS) AF: 0.000288 AC: 20 AN: 69528

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 35626

Middle Eastern (MID) AF: 0.000214 AC: 1 AN: 4682

European-Non Finnish (NFE) AF: 0.0000396 AC: 39 AN: 985260

Other (OTH) AF: 0.000150 AC: 8 AN: 53316

GnomAD4 genome AF: 0.0000539 AC: 8 AN: 148354 Hom.: 0 Cov.: 0 AF XY: 0.0000277 AC XY: 2 AN XY: 72076

African (AFR) AF: 0.0000996 AC: 4 AN: 40166

American (AMR) AF: 0.0000673 AC: 1 AN: 14856

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3430

East Asian (EAS) AF: 0.00 AC: 0 AN: 4984

South Asian (SAS) AF: 0.00 AC: 0 AN: 4424

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10164

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 312

European-Non Finnish (NFE) AF: 0.0000149 AC: 1 AN: 67114

Other (OTH) AF: 0.000999 AC: 2 AN: 2002

Alfa AF: 0.00 Hom.: 1588

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
PhyloP100		-0.77

Splicing

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

Other links and lift over

dbSNP: rs11279828; hg19: chr5-167858462;