Variant rs2286394 details in Genebe, Genetics Data Aggregator

Variant summary

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

The NM_017706.5(WDR55):c.629C>T(p.Ser210Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.226 in 1,614,056 control chromosomes in the GnomAD database, including 42,672 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. Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.

Frequency

Genomes: 𝑓 0.19 ( 3342 hom., cov: 32)

Exomes 𝑓: 0.23 ( 39330 hom. )

Consequence

WDR55
NM_017706.5 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.35

Variant links:

Genes affected

WDR55 (HGNC:25971): (WD repeat domain 55) Predicted to be involved in rRNA processing. Located in nucleolus and nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]

WDR55 links:

WDR55 (HGNC:):

WDR55 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 (MetaRNN=0.0019042492).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.291 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
WDR55	NM_017706.5 linkuse as main transcript	c.629C>T	p.Ser210Phe	missense_variant	5/7	ENST00000358337.10	NP_060176.3	Q9H6Y2-1
WDR55	XM_005268469.4 linkuse as main transcript	c.629C>T	p.Ser210Phe	missense_variant	5/8		XP_005268526.1	Q9H6Y2-1
WDR55	XM_017009600.3 linkuse as main transcript	c.146C>T	p.Ser49Phe	missense_variant	6/8		XP_016865089.1	G3V1J0

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
WDR55	ENST00000358337.10 linkuse as main transcript	c.629C>T	p.Ser210Phe	missense_variant	5/7	1	NM_017706.5	ENSP00000351100.5		Q9H6Y2-1

Frequencies

GnomAD3 genomes

AF:

0.193

AC:

29320

AN:

152088

Hom.:

3326

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0786

Gnomad AMI

AF:

0.0440

Gnomad AMR

AF:

0.230

Gnomad ASJ

AF:

0.212

Gnomad EAS

AF:

0.304

Gnomad SAS

AF:

0.253

Gnomad FIN

AF:

0.261

Gnomad MID

AF:

0.168

Gnomad NFE

AF:

0.231

Gnomad OTH

AF:

0.207

GnomAD3 exomes

AF:

0.237

AC:

59619

AN:

251404

Hom.:

7479

AF XY:

0.239

AC XY:

32520

AN XY:

135888

show subpopulations

Gnomad AFR exome

AF:

0.0738

Gnomad AMR exome

AF:

0.247

Gnomad ASJ exome

AF:

0.213

Gnomad EAS exome

AF:

0.306

Gnomad SAS exome

AF:

0.256

Gnomad FIN exome

AF:

0.273

Gnomad NFE exome

AF:

0.237

Gnomad OTH exome

AF:

0.239

GnomAD4 exome

AF:

0.229

AC:

334992

AN:

1461850

Hom.:

39330

Cov.:

AF XY:

0.231

AC XY:

167651

AN XY:

727226

show subpopulations

Gnomad4 AFR exome

AF:

0.0748

Gnomad4 AMR exome

AF:

0.247

Gnomad4 ASJ exome

AF:

0.207

Gnomad4 EAS exome

AF:

0.296

Gnomad4 SAS exome

AF:

0.252

Gnomad4 FIN exome

AF:

0.272

Gnomad4 NFE exome

AF:

0.227

Gnomad4 OTH exome

AF:

0.229

GnomAD4 genome

AF:

0.193

AC:

29345

AN:

152206

Hom.:

3342

Cov.:

AF XY:

0.194

AC XY:

14468

AN XY:

74416

show subpopulations

Gnomad4 AFR

AF:

0.0783

Gnomad4 AMR

AF:

0.232

Gnomad4 ASJ

AF:

0.212

Gnomad4 EAS

AF:

0.303

Gnomad4 SAS

AF:

0.253

Gnomad4 FIN

AF:

0.261

Gnomad4 NFE

AF:

0.231

Gnomad4 OTH

AF:

0.212

Alfa

AF:

0.223

Hom.:

9629

Bravo

AF:

0.183

TwinsUK

AF:

0.219

AC:

811

ALSPAC

AF:

0.225

AC:

866

ESP6500AA

AF:

0.0763

AC:

336

ESP6500EA

AF:

0.234

AC:

2014

ExAC

AF:

0.236

AC:

28601

Asia WGS

AF:

0.319

AC:

1108

AN:

3478

EpiCase

AF:

0.221

EpiControl

AF:

0.217

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.33

BayesDel_addAF

Benign

-0.60

BayesDel_noAF

Benign

-0.49

CADD

Pathogenic

DANN

Uncertain

1.0

DEOGEN2

Benign

0.40

Eigen

Uncertain

0.28

Eigen_PC

Uncertain

0.27

FATHMM_MKL

Benign

0.76

LIST_S2

Uncertain

0.90

MetaRNN

Benign

0.0019

MetaSVM

Benign

-1.0

MutationAssessor

Benign

1.6

PrimateAI

Uncertain

0.58

PROVEAN

Uncertain

-3.8

REVEL

Benign

0.050

Sift

Uncertain

0.017

Sift4G

Uncertain

0.018

Polyphen

0.99

Vest4

0.16

MPC

0.70

ClinPred

0.019

GERP RS

3.5

Varity_R

0.12

gMVP

0.32

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.030

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over