rs4976593

Variant names:

• chr5-168350438-G-A
• rs4976593
• NM_015238.3:c.120-20986G>A

Your query was ambiguous. Multiple possible variants found:

• chr5-168350438-G-A
• chr5-168350438-G-C
• chr5-168350438-G-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_015238.3(WWC1):​c.120-20986G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.608 in 151,984 control chromosomes in the GnomAD database, including 29,519 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.61 (29519 hom., cov: 31)
• Consequence: WWC1 NM_015238.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0380
• 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]

ENSG00000296528 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.805 is higher than 0.05.

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.120-20986G>A		intron	N/A	NP_056053.1	Q8IX03-1
	WWC1	NM_001161661.2		c.120-20986G>A		intron	N/A	NP_001155133.1	Q8IX03-2
	WWC1	NM_001161662.2		c.120-20986G>A		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.120-20986G>A		intron	N/A	ENSP00000265293.4	Q8IX03-1
	WWC1	ENST00000917779.1		c.120-20986G>A		intron	N/A	ENSP00000587838.1
	WWC1	ENST00000917783.1		c.120-20986G>A		intron	N/A	ENSP00000587842.1

Frequencies

GnomAD3 genomes AF: 0.608 AC: 92351 AN: 151866 Hom.: 29499 Cov.: 31

Gnomad AFR AF: 0.402

Gnomad AMI AF: 0.683

Gnomad AMR AF: 0.709

Gnomad ASJ AF: 0.623

Gnomad EAS AF: 0.825

Gnomad SAS AF: 0.734

Gnomad FIN AF: 0.689

Gnomad MID AF: 0.570

Gnomad NFE AF: 0.671

Gnomad OTH AF: 0.621

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

GnomAD4 genome AF: 0.608 AC: 92407 AN: 151984 Hom.: 29519 Cov.: 31 AF XY: 0.611 AC XY: 45419 AN XY: 74298

African (AFR) AF: 0.402 AC: 16656 AN: 41432

American (AMR) AF: 0.710 AC: 10837 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.623 AC: 2159 AN: 3466

East Asian (EAS) AF: 0.826 AC: 4251 AN: 5146

South Asian (SAS) AF: 0.734 AC: 3533 AN: 4812

European-Finnish (FIN) AF: 0.689 AC: 7285 AN: 10578

Middle Eastern (MID) AF: 0.571 AC: 168 AN: 294

European-Non Finnish (NFE) AF: 0.671 AC: 45583 AN: 67964

Other (OTH) AF: 0.623 AC: 1315 AN: 2112

Alfa AF: 0.656 Hom.: 24096

Bravo AF: 0.602

Asia WGS AF: 0.744 AC: 2584 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.78
DANN	Benign	0.37
PhyloP100		-0.038
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs4976593; hg19: chr5-167777443;