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

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBA1

The NM_015238.3(WWC1):c.2280+57_2280+60delGCTG variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.387 in 1,406,984 control chromosomes in the GnomAD database, including 105,519 homozygotes. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.38 ( 11745 hom., cov: 0)

Exomes 𝑓: 0.39 ( 93774 hom. )

Consequence

WWC1
NM_015238.3 intron

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.527

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:

WWC1 (HGNC:):

WWC1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP6

Variant 5-168431457-TCTGG-T is Benign according to our data. Variant chr5-168431457-TCTGG-T is described in ClinVar as [Benign]. Clinvar id is 403611.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.458 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
WWC1	NM_015238.3 linkuse as main transcript	c.2280+57_2280+60delGCTG		intron_variant		ENST00000265293.9	NP_056053.1	Q8IX03-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
WWC1	ENST00000265293.9 linkuse as main transcript	c.2280+57_2280+60delGCTG		intron_variant		1	NM_015238.3	ENSP00000265293.4		Q8IX03-1

Frequencies

GnomAD3 genomes

AF:

0.384

AC:

56792

AN:

148060

Hom.:

11741

Cov.:

show subpopulations

Gnomad AFR

AF:

0.244

Gnomad AMI

AF:

0.344

Gnomad AMR

AF:

0.391

Gnomad ASJ

AF:

0.424

Gnomad EAS

AF:

0.193

Gnomad SAS

AF:

0.402

Gnomad FIN

AF:

0.467

Gnomad MID

AF:

0.484

Gnomad NFE

AF:

0.463

Gnomad OTH

AF:

0.428

GnomAD3 exomes

AF:

0.349

AC:

44091

AN:

126504

Hom.:

8000

AF XY:

0.357

AC XY:

24246

AN XY:

68006

show subpopulations

Gnomad AFR exome

AF:

0.210

Gnomad AMR exome

AF:

0.313

Gnomad ASJ exome

AF:

0.365

Gnomad EAS exome

AF:

0.186

Gnomad SAS exome

AF:

0.370

Gnomad FIN exome

AF:

0.376

Gnomad NFE exome

AF:

0.401

Gnomad OTH exome

AF:

0.392

GnomAD4 exome

AF:

0.388

AC:

488354

AN:

1258818

Hom.:

93774

AF XY:

0.390

AC XY:

243934

AN XY:

624868

show subpopulations

Gnomad4 AFR exome

AF:

0.223

Gnomad4 AMR exome

AF:

0.310

Gnomad4 ASJ exome

AF:

0.394

Gnomad4 EAS exome

AF:

0.221

Gnomad4 SAS exome

AF:

0.379

Gnomad4 FIN exome

AF:

0.411

Gnomad4 NFE exome

AF:

0.401

Gnomad4 OTH exome

AF:

0.389

GnomAD4 genome

AF:

0.383

AC:

56818

AN:

148166

Hom.:

11745

Cov.:

AF XY:

0.381

AC XY:

27476

AN XY:

72038

show subpopulations

Gnomad4 AFR

AF:

0.244

Gnomad4 AMR

AF:

0.391

Gnomad4 ASJ

AF:

0.424

Gnomad4 EAS

AF:

0.192

Gnomad4 SAS

AF:

0.403

Gnomad4 FIN

AF:

0.467

Gnomad4 NFE

AF:

0.463

Gnomad4 OTH

AF:

0.429

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not specified

Benign:1

Benign, criteria provided, single submitter

clinical testing

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Mar 28, 2016

Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: Frequency -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

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