Variant 16-651217-G-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2

The NM_145294.5(WDR90):c.687G>T(p.Leu229Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00606 in 1,613,174 control chromosomes in the GnomAD database, including 43 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0040 ( 3 hom., cov: 33)

Exomes 𝑓: 0.0063 ( 40 hom. )

Consequence

WDR90
NM_145294.5 missense

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: -2.30

Variant links:

Genes affected

WDR90 (HGNC:26960): (WD repeat domain 90) Involved in cilium assembly. Located in centriole. [provided by Alliance of Genome Resources, Apr 2022]

WDR90 links:

WDR90 (HGNC:):

WDR90 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.0032508075).

BP6

Variant 16-651217-G-T is Benign according to our data. Variant chr16-651217-G-T is described in ClinVar as [Likely_benign]. Clinvar id is 2645836.Status of the report is criteria_provided_single_submitter, 1 stars.

BS2

High Homozygotes in GnomAd4 at 3 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
WDR90	NM_145294.5 linkuse as main transcript	c.687G>T	p.Leu229Phe	missense_variant	7/41	ENST00000293879.9	NP_660337.3	Q96KV7-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
WDR90	ENST00000293879.9 linkuse as main transcript	c.687G>T	p.Leu229Phe	missense_variant	7/41	5	NM_145294.5	ENSP00000293879.4		Q96KV7-1

Frequencies

GnomAD3 genomes

AF:

0.00399

AC:

607

AN:

152198

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00109

Gnomad AMI

AF:

0.0307

Gnomad AMR

AF:

0.00137

Gnomad ASJ

AF:

0.00490

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00704

Gnomad FIN

AF:

0.0000942

Gnomad MID

AF:

0.00316

Gnomad NFE

AF:

0.00669

Gnomad OTH

AF:

0.00240

GnomAD3 exomes

AF:

0.00414

AC:

1029

AN:

248390

Hom.:

AF XY:

0.00444

AC XY:

600

AN XY:

135152

show subpopulations

Gnomad AFR exome

AF:

0.00104

Gnomad AMR exome

AF:

0.00157

Gnomad ASJ exome

AF:

0.00280

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00546

Gnomad FIN exome

AF:

0.000186

Gnomad NFE exome

AF:

0.00659

Gnomad OTH exome

AF:

0.00315

GnomAD4 exome

AF:

0.00628

AC:

9169

AN:

1460858

Hom.:

Cov.:

AF XY:

0.00627

AC XY:

4555

AN XY:

726730

show subpopulations

Gnomad4 AFR exome

AF:

0.000717

Gnomad4 AMR exome

AF:

0.00161

Gnomad4 ASJ exome

AF:

0.00275

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.00538

Gnomad4 FIN exome

AF:

0.000248

Gnomad4 NFE exome

AF:

0.00740

Gnomad4 OTH exome

AF:

0.00475

GnomAD4 genome

AF:

0.00398

AC:

606

AN:

152316

Hom.:

Cov.:

AF XY:

0.00381

AC XY:

284

AN XY:

74482

show subpopulations

Gnomad4 AFR

AF:

0.00108

Gnomad4 AMR

AF:

0.00137

Gnomad4 ASJ

AF:

0.00490

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00704

Gnomad4 FIN

AF:

0.0000942

Gnomad4 NFE

AF:

0.00669

Gnomad4 OTH

AF:

0.00237

Alfa

AF:

0.00549

Hom.:

Bravo

AF:

0.00391

TwinsUK

AF:

0.00728

AC:

ALSPAC

AF:

0.00908

AC:

ESP6500AA

AF:

0.00101

AC:

ESP6500EA

AF:

0.00495

AC:

ExAC

AF:

0.00414

AC:

500

Asia WGS

AF:

0.00115

AC:

AN:

3478

EpiCase

AF:

0.00600

EpiControl

AF:

0.00587

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

CeGaT Center for Human Genetics Tuebingen

Mar 01, 2023

WDR90: BP4, BS2 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.082

BayesDel_addAF

Benign

-0.74

BayesDel_noAF

Benign

-0.83

CADD

Benign

0.012

DANN

Benign

0.49

DEOGEN2

Benign

0.011

T;T

Eigen

Benign

-1.6

Eigen_PC

Benign

-1.7

FATHMM_MKL

Benign

0.0099

LIST_S2

Benign

0.48

T;T

M_CAP

Benign

0.0058

MetaRNN

Benign

0.0033

T;T

MetaSVM

Benign

-1.0

MutationAssessor

Benign

1.1

.;L

PrimateAI

Benign

0.24

PROVEAN

Benign

-0.18

N;N

REVEL

Benign

0.020

Sift

Benign

0.62

T;T

Sift4G

Benign

0.34

T;T

Polyphen

0.0040

.;B

Vest4

0.085

MutPred

0.34

Loss of stability (P = 0.086);Loss of stability (P = 0.086);

MVP

0.014

MPC

0.16

ClinPred

0.00058

GERP RS

-9.3

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

Varity_R

0.039

gMVP

0.070

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

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