Variant rs7163367 details in Genebe, Genetics Data Aggregator

Variant summary

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

The ENST00000268130.12(WDR93):c.760T>A(p.Ser254Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.426 in 1,555,692 control chromosomes in the GnomAD database, including 145,383 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict 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 0.42 ( 14008 hom., cov: 32)

Exomes 𝑓: 0.43 ( 131375 hom. )

Consequence

WDR93
ENST00000268130.12 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.440

Variant links:

Genes affected

WDR93 (HGNC:26924): (WD repeat domain 93) Predicted to enable oxidoreductase activity, acting on NAD(P)H. Predicted to be involved in electron transport chain. Predicted to be part of mitochondrial respiratory chain complex I. [provided by Alliance of Genome Resources, Apr 2022]

WDR93 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=1.1756467E-4).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.479 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
WDR93	NM_020212.2 linkuse as main transcript	c.760T>A	p.Ser254Thr	missense_variant	7/17	ENST00000268130.12	NP_064597.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
WDR93	ENST00000268130.12 linkuse as main transcript	c.760T>A	p.Ser254Thr	missense_variant	7/17	1	NM_020212.2	ENSP00000268130	P2	Q6P2C0-1
WDR93	ENST00000560294.5 linkuse as main transcript	c.760T>A	p.Ser254Thr	missense_variant	7/17	2		ENSP00000453971	A2	Q6P2C0-2

Frequencies

GnomAD3 genomes

AF:

0.421

AC:

63953

AN:

151866

Hom.:

13991

Cov.:

show subpopulations

Gnomad AFR

AF:

0.485

Gnomad AMI

AF:

0.666

Gnomad AMR

AF:

0.331

Gnomad ASJ

AF:

0.450

Gnomad EAS

AF:

0.214

Gnomad SAS

AF:

0.412

Gnomad FIN

AF:

0.273

Gnomad MID

AF:

0.373

Gnomad NFE

AF:

0.438

Gnomad OTH

AF:

0.398

GnomAD3 exomes

AF:

0.377

AC:

83817

AN:

222306

Hom.:

17116

AF XY:

0.384

AC XY:

46428

AN XY:

120874

show subpopulations

Gnomad AFR exome

AF:

0.476

Gnomad AMR exome

AF:

0.243

Gnomad ASJ exome

AF:

0.443

Gnomad EAS exome

AF:

0.194

Gnomad SAS exome

AF:

0.405

Gnomad FIN exome

AF:

0.281

Gnomad NFE exome

AF:

0.434

Gnomad OTH exome

AF:

0.385

GnomAD4 exome

AF:

0.427

AC:

598829

AN:

1403710

Hom.:

131375

Cov.:

AF XY:

0.426

AC XY:

297563

AN XY:

697730

show subpopulations

Gnomad4 AFR exome

AF:

0.475

Gnomad4 AMR exome

AF:

0.257

Gnomad4 ASJ exome

AF:

0.439

Gnomad4 EAS exome

AF:

0.229

Gnomad4 SAS exome

AF:

0.410

Gnomad4 FIN exome

AF:

0.292

Gnomad4 NFE exome

AF:

0.446

Gnomad4 OTH exome

AF:

0.416

GnomAD4 genome

AF:

0.421

AC:

64023

AN:

151982

Hom.:

14008

Cov.:

AF XY:

0.411

AC XY:

30569

AN XY:

74298

show subpopulations

Gnomad4 AFR

AF:

0.485

Gnomad4 AMR

AF:

0.331

Gnomad4 ASJ

AF:

0.450

Gnomad4 EAS

AF:

0.215

Gnomad4 SAS

AF:

0.411

Gnomad4 FIN

AF:

0.273

Gnomad4 NFE

AF:

0.438

Gnomad4 OTH

AF:

0.397

Alfa

AF:

0.430

Hom.:

11198

Bravo

AF:

0.425

TwinsUK

AF:

0.465

AC:

1726

ALSPAC

AF:

0.447

AC:

1721

ESP6500AA

AF:

0.471

AC:

2074

ESP6500EA

AF:

0.441

AC:

3788

ExAC

AF:

0.391

AC:

47502

Asia WGS

AF:

0.341

AC:

1191

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.057

BayesDel_addAF

Benign

-0.84

BayesDel_noAF

Benign

-0.83

CADD

Benign

0.090

DANN

Benign

0.36

DEOGEN2

Benign

0.0016

T;.

Eigen

Benign

-1.8

Eigen_PC

Benign

-1.8

FATHMM_MKL

Benign

0.00029

LIST_S2

Benign

0.13

T;T

MetaRNN

Benign

0.00012

T;T

MetaSVM

Benign

-0.99

MutationAssessor

Benign

-0.95

N;N

MutationTaster

Benign

1.0

P;P

PrimateAI

Benign

0.35

PROVEAN

Benign

1.4

N;N

REVEL

Benign

0.020

Sift

Benign

1.0

T;T

Sift4G

Benign

1.0

T;T

Polyphen

0.0

B;B

Vest4

0.014

MPC

0.065

ClinPred

0.0027

GERP RS

-2.3

Varity_R

0.043

gMVP

0.16

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over