Variant rs10817479 details in Genebe, Genetics Data Aggregator

Variant summary

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

The ENST00000374193.9(WDR31):c.337C>T(p.Pro113Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0637 in 1,613,630 control chromosomes in the GnomAD database, including 3,677 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 0.052 ( 287 hom., cov: 32)

Exomes 𝑓: 0.065 ( 3390 hom. )

Consequence

WDR31
ENST00000374193.9 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.927

Variant links:

Genes affected

WDR31 (HGNC:21421): (WD repeat domain 31) This gene encodes a member of the WD repeat protein family. WD repeats are minimally conserved regions of approximately 40 amino acids typically bracketed by gly-his and trp-asp (GH-WD), which may facilitate formation of heterotrimeric or multiprotein complexes. Members of this family are involved in a variety of cellular processes, including cell cycle progression, signal transduction, apoptosis, and gene regulation. Multiple alternatively spliced transcript variants encoding distinct isoforms have been found for this gene but the biological validity of some variants has not been determined. [provided by RefSeq, Jul 2008]

WDR31 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.001717329).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.134 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
WDR31	NM_001012361.4 linkuse as main transcript	c.337C>T	p.Pro113Ser	missense_variant	6/11	ENST00000374193.9	NP_001012361.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
WDR31	ENST00000374193.9 linkuse as main transcript	c.337C>T	p.Pro113Ser	missense_variant	6/11	1	NM_001012361.4	ENSP00000363308	P4	Q8NA23-1

Frequencies

GnomAD3 genomes

AF:

0.0523

AC:

7962

AN:

152134

Hom.:

287

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0127

Gnomad AMI

AF:

0.0844

Gnomad AMR

AF:

0.0677

Gnomad ASJ

AF:

0.0484

Gnomad EAS

AF:

0.143

Gnomad SAS

AF:

0.0573

Gnomad FIN

AF:

0.0605

Gnomad MID

AF:

0.0380

Gnomad NFE

AF:

0.0639

Gnomad OTH

AF:

0.0680

GnomAD3 exomes

AF:

0.0676

AC:

16933

AN:

250538

Hom.:

720

AF XY:

0.0659

AC XY:

8917

AN XY:

135358

show subpopulations

Gnomad AFR exome

AF:

0.0114

Gnomad AMR exome

AF:

0.0992

Gnomad ASJ exome

AF:

0.0482

Gnomad EAS exome

AF:

0.138

Gnomad SAS exome

AF:

0.0538

Gnomad FIN exome

AF:

0.0610

Gnomad NFE exome

AF:

0.0617

Gnomad OTH exome

AF:

0.0604

GnomAD4 exome

AF:

0.0649

AC:

94838

AN:

1461378

Hom.:

3390

Cov.:

AF XY:

0.0645

AC XY:

46901

AN XY:

726976

show subpopulations

Gnomad4 AFR exome

AF:

0.0102

Gnomad4 AMR exome

AF:

0.0949

Gnomad4 ASJ exome

AF:

0.0489

Gnomad4 EAS exome

AF:

0.151

Gnomad4 SAS exome

AF:

0.0570

Gnomad4 FIN exome

AF:

0.0597

Gnomad4 NFE exome

AF:

0.0634

Gnomad4 OTH exome

AF:

0.0659

GnomAD4 genome

AF:

0.0523

AC:

7957

AN:

152252

Hom.:

287

Cov.:

AF XY:

0.0527

AC XY:

3926

AN XY:

74454

show subpopulations

Gnomad4 AFR

AF:

0.0126

Gnomad4 AMR

AF:

0.0675

Gnomad4 ASJ

AF:

0.0484

Gnomad4 EAS

AF:

0.143

Gnomad4 SAS

AF:

0.0569

Gnomad4 FIN

AF:

0.0605

Gnomad4 NFE

AF:

0.0639

Gnomad4 OTH

AF:

0.0673

Alfa

AF:

0.0631

Hom.:

878

Bravo

AF:

0.0521

TwinsUK

AF:

0.0677

AC:

251

ALSPAC

AF:

0.0734

AC:

283

ESP6500AA

AF:

0.0161

AC:

ESP6500EA

AF:

0.0665

AC:

572

ExAC

AF:

0.0648

AC:

7872

Asia WGS

AF:

0.0830

AC:

292

AN:

3478

EpiCase

AF:

0.0632

EpiControl

AF:

0.0623

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.097

BayesDel_addAF

Benign

-0.66

BayesDel_noAF

Benign

-0.59

CADD

Benign

DANN

Benign

0.36

DEOGEN2

Benign

0.0088

.;T;.;.

Eigen

Benign

-0.74

Eigen_PC

Benign

-0.75

FATHMM_MKL

Benign

0.12

LIST_S2

Benign

0.61

.;T;T;T

MetaRNN

Benign

0.0017

T;T;T;T

MetaSVM

Benign

-1.1

MutationAssessor

Benign

1.8

.;L;.;.

MutationTaster

Benign

1.0

N;N;N

PrimateAI

Benign

0.25

PROVEAN

Benign

-2.2

N;N;.;D

REVEL

Benign

0.068

Sift

Benign

0.43

T;T;.;T

Sift4G

Benign

0.41

T;T;T;T

Polyphen

0.017

B;B;B;.

Vest4

0.035

MPC

0.11

ClinPred

0.0016

GERP RS

1.8

Varity_R

0.057

gMVP

0.19

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