Variant 16-650988-C-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.560-7C>T variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00394 in 1,612,946 control chromosomes in the GnomAD database, including 32 homozygotes. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0027 ( 3 hom., cov: 33)

Exomes 𝑓: 0.0041 ( 29 hom. )

Consequence

WDR90
NM_145294.5 splice_region, intron

Scores

Splicing: ADA: 0.00001472

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: -1.49

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:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.91).

BP6

Variant 16-650988-C-T is Benign according to our data. Variant chr16-650988-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 2645835.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.560-7C>T		splice_region_variant, intron_variant		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.560-7C>T		splice_region_variant, intron_variant		5	NM_145294.5	ENSP00000293879.4		Q96KV7-1

Frequencies

GnomAD3 genomes

AF:

0.00274

AC:

417

AN:

152212

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000482

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00249

Gnomad ASJ

AF:

0.00317

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00827

Gnomad FIN

AF:

0.000565

Gnomad MID

AF:

0.0158

Gnomad NFE

AF:

0.00432

Gnomad OTH

AF:

0.00144

GnomAD3 exomes

AF:

0.00375

AC:

933

AN:

248876

Hom.:

AF XY:

0.00420

AC XY:

568

AN XY:

135186

show subpopulations

Gnomad AFR exome

AF:

0.000388

Gnomad AMR exome

AF:

0.000985

Gnomad ASJ exome

AF:

0.00259

Gnomad EAS exome

AF:

0.000111

Gnomad SAS exome

AF:

0.00830

Gnomad FIN exome

AF:

0.000465

Gnomad NFE exome

AF:

0.00512

Gnomad OTH exome

AF:

0.00397

GnomAD4 exome

AF:

0.00407

AC:

5944

AN:

1460616

Hom.:

Cov.:

AF XY:

0.00426

AC XY:

3094

AN XY:

726610

show subpopulations

Gnomad4 AFR exome

AF:

0.000597

Gnomad4 AMR exome

AF:

0.00136

Gnomad4 ASJ exome

AF:

0.00283

Gnomad4 EAS exome

AF:

0.0000756

Gnomad4 SAS exome

AF:

0.00919

Gnomad4 FIN exome

AF:

0.000573

Gnomad4 NFE exome

AF:

0.00420

Gnomad4 OTH exome

AF:

0.00386

GnomAD4 genome

AF:

0.00272

AC:

414

AN:

152330

Hom.:

Cov.:

AF XY:

0.00258

AC XY:

192

AN XY:

74488

show subpopulations

Gnomad4 AFR

AF:

0.000481

Gnomad4 AMR

AF:

0.00248

Gnomad4 ASJ

AF:

0.00317

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00828

Gnomad4 FIN

AF:

0.000565

Gnomad4 NFE

AF:

0.00432

Gnomad4 OTH

AF:

0.00142

Alfa

AF:

0.00356

Hom.:

Bravo

AF:

0.00266

Asia WGS

AF:

0.00462

AC:

AN:

3478

EpiCase

AF:

0.00594

EpiControl

AF:

0.00516

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

BayesDel_noAF

Benign

-0.91

CADD

Benign

0.24

DANN

Benign

0.48

Splicing

Name

Calibrated prediction

Score

Prediction

dbscSNV1_ADA

Benign

0.000015

dbscSNV1_RF

Benign

0.0020

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