Variant 5-168418786-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_015238.3(WWC1):c.1185-3222C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.433 in 151,876 control chromosomes in the GnomAD database, including 15,691 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as association (no stars).

Frequency

Genomes: 𝑓 0.43 ( 15691 hom., cov: 31)

Consequence

WWC1
NM_015238.3 intron

Scores

Clinical Significance

association no assertion criteria provided O:1

Conservation

PhyloP100: 0.343

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:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.85).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.75 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
WWC1	NM_015238.3 linkuse as main transcript	c.1185-3222C>T		intron_variant		ENST00000265293.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
WWC1	ENST00000265293.9 linkuse as main transcript	c.1185-3222C>T		intron_variant		1	NM_015238.3	P1	Q8IX03-1

Frequencies

GnomAD3 genomes

AF:

0.433

AC:

65656

AN:

151758

Hom.:

15641

Cov.:

show subpopulations

Gnomad AFR

AF:

0.584

Gnomad AMI

AF:

0.486

Gnomad AMR

AF:

0.499

Gnomad ASJ

AF:

0.331

Gnomad EAS

AF:

0.769

Gnomad SAS

AF:

0.300

Gnomad FIN

AF:

0.419

Gnomad MID

AF:

0.351

Gnomad NFE

AF:

0.318

Gnomad OTH

AF:

0.394

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

GnomAD4 genome

AF:

0.433

AC:

65773

AN:

151876

Hom.:

15691

Cov.:

AF XY:

0.436

AC XY:

32379

AN XY:

74212

show subpopulations

Gnomad4 AFR

AF:

0.585

Gnomad4 AMR

AF:

0.500

Gnomad4 ASJ

AF:

0.331

Gnomad4 EAS

AF:

0.770

Gnomad4 SAS

AF:

0.300

Gnomad4 FIN

AF:

0.419

Gnomad4 NFE

AF:

0.318

Gnomad4 OTH

AF:

0.399

Alfa

AF:

0.387

Hom.:

5399

Bravo

AF:

0.455

Asia WGS

AF:

0.523

AC:

1817

AN:

3478

ClinVar

Significance: association

Submissions summary: Other:1

Revision: no assertion criteria provided

LINK: link

Submissions by phenotype

Memory quantitative trait locus

Other:1

association, no assertion criteria provided

literature only

OMIM

Aug 07, 2013

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.85

CADD

Benign

5.0

DANN

Benign

0.60

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

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over