Variant 5-168431457-TCTGGCTGGCTGGCTGGCTGGCTGGCTGG-TCTGGCTGGCTGGCTGGCTGGCTGGCTGGCTGG details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 0P and 0B.

The NM_015238.3(WWC1):c.2280+57_2280+60dup 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

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.765

Variant links:

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 links:

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 0 ACMG points.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
WWC1	NM_015238.3 linkuse as main transcript	c.2280+57_2280+60dup		intron_variant		ENST00000265293.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
WWC1	ENST00000265293.9 linkuse as main transcript	c.2280+57_2280+60dup		intron_variant		1	NM_015238.3	P1	Q8IX03-1

Frequencies

GnomAD3 genomes

AF:

0.00208

AC:

309

AN:

148352

Hom.:

Cov.:

show subpopulations

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.:

AF XY:

0.00262

AC XY:

178

AN XY:

68006

show subpopulations

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.:

Cov.:

AF XY:

0.00229

AC XY:

1439

AN XY:

628320

show subpopulations

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.:

Cov.:

AF XY:

0.00194

AC XY:

140

AN XY:

72194

show subpopulations

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

Name

Calibrated prediction

Score

Prediction

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over