5-168431457-TCTGGCTGGCTGGCTGGCTGGCTGGCTGGCTGG-TCTGGCTGGCTGGCTGGCTGG

Variant names:

• chr5-168431476-GGCTGGCTGGCTG-G
• NM_015238.3:c.2280+49_2280+60delGCTGGCTGGCTG

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+60delGCTGGCTGGCTG variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. It is difficult to determine the true allele frequency of this variant because it is of type DEL_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: not found (cov: 31)
• Consequence: WWC1 NM_015238.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.648
• 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+49_2280+60delGCTGGCTGGCTG		intron	N/A	NP_056053.1	Q8IX03-1
	WWC1	NM_001161661.2		c.2280+49_2280+60delGCTGGCTGGCTG		intron	N/A	NP_001155133.1	Q8IX03-2
	WWC1	NM_001161662.2		c.2280+49_2280+60delGCTGGCTGGCTG		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+33_2280+44delGCTGGCTGGCTG		intron	N/A	ENSP00000265293.4	Q8IX03-1
	WWC1	ENST00000393895.7	TSL:1	c.2163+33_2163+44delGCTGGCTGGCTG		intron	N/A	ENSP00000377473.3	H3BLZ3
	WWC1	ENST00000524228.5	TSL:1	c.1608+33_1608+44delGCTGGCTGGCTG		intron	N/A	ENSP00000429339.1	H0YBE8

Frequencies

GnomAD3 genomes Cov.: 31

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome Cov.: 31

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		0.65

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

hg19: chr5-167858481;