NM_015238.3:c.2280+33_2280+60dupGCTGGCTGGCTGGCTGGCTGGCTGGCTG

Variant names:

• chr5-168431457-T-TCTGGCTGGCTGGCTGGCTGGCTGGCTGG
• rs11279828
• NM_015238.3:c.2280+33_2280+60dupGCTGGCTGGCTGGCTGGCTGGCTGGCTG

Variant summary

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

The NM_015238.3(WWC1):​c.2280+33_2280+60dupGCTGGCTGGCTGGCTGGCTGGCTGGCTG 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 0.0000067 (0 hom., cov: 0)
• Consequence: WWC1 NM_015238.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.765
• Publications: 0 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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_015238.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	WWC1	NM_015238.3	MANE Select	c.2280+33_2280+60dupGCTGGCTGGCTGGCTGGCTGGCTGGCTG		intron	N/A	NP_056053.1
	WWC1	NM_001161661.2		c.2280+33_2280+60dupGCTGGCTGGCTGGCTGGCTGGCTGGCTG		intron	N/A	NP_001155133.1
	WWC1	NM_001161662.2		c.2280+33_2280+60dupGCTGGCTGGCTGGCTGGCTGGCTGGCTG		intron	N/A	NP_001155134.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	WWC1	ENST00000265293.9	TSL:1 MANE Select	c.2280+13_2280+14insCTGGCTGGCTGGCTGGCTGGCTGGCTGG		intron	N/A	ENSP00000265293.4
	WWC1	ENST00000393895.7	TSL:1	c.2163+13_2163+14insCTGGCTGGCTGGCTGGCTGGCTGGCTGG		intron	N/A	ENSP00000377473.3
	WWC1	ENST00000524228.5	TSL:1	c.1608+13_1608+14insCTGGCTGGCTGGCTGGCTGGCTGGCTGG		intron	N/A	ENSP00000429339.1

Frequencies

GnomAD3 genomes AF: 0.00000674 AC: 1 AN: 148354 Hom.: 0 Cov.: 0

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: 0.000226

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00

Gnomad OTH AF: 0.00

GnomAD4 exome Cov.: 0

GnomAD4 genome AF: 0.00000674 AC: 1 AN: 148464 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 72196

African (AFR) AF: 0.00 AC: 0 AN: 40282

American (AMR) AF: 0.00 AC: 0 AN: 14876

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

East Asian (EAS) AF: 0.00 AC: 0 AN: 4972

South Asian (SAS) AF: 0.000226 AC: 1 AN: 4420

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

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 290

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 67104

Other (OTH) AF: 0.00 AC: 0 AN: 2024

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

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;