Variant chr8-144108637-G-A 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_001316309.2(WDR97):c.571G>A(p.Val191Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00528 in 700,518 control chromosomes in the GnomAD database, including 18 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/17 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0044 ( 3 hom., cov: 35)

Exomes 𝑓: 0.0055 ( 15 hom. )

Consequence

WDR97
NM_001316309.2 missense

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.998

Variant links:

Genes affected

WDR97 (HGNC:26959): (WD repeat domain 97) The function and protein-coding potential of this gene is unknown. The exon combination is based on AB058778.1 for which two possible open reading frames can be predicted (with start codons at nucleotide 26 or 2614). The position of the first ORF stop codon is consistent with a prediction of nonsense-mediated decay. Given the observation of the first ORF and its length, a predicted translation of the second ORF is inconsistent with the translation leaky scanning theory. Therefore, this gene is represented as a non-protein-coding transcript. [provided by RefSeq, Oct 2008]

WDR97 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=0.0051650107).

BP6

Variant 8-144108637-G-A is Benign according to our data. Variant chr8-144108637-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 2658972.Status of the report is criteria_provided_single_submitter, 1 stars.

BS2

High Homozygotes in GnomAd4 at 3 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
WDR97	NM_001316309.2 linkuse as main transcript	c.571G>A	p.Val191Met	missense_variant	3/24	ENST00000323662.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
WDR97	ENST00000323662.9 linkuse as main transcript	c.571G>A	p.Val191Met	missense_variant	3/24	5	NM_001316309.2	P1	A6NE52-1
WDR97	ENST00000534167.5 linkuse as main transcript	c.571G>A	p.Val191Met	missense_variant, NMD_transcript_variant	3/23	1

Frequencies

GnomAD3 genomes

AF:

0.00439

AC:

668

AN:

152232

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000965

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00504

Gnomad ASJ

AF:

0.00375

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00455

Gnomad FIN

AF:

0.00179

Gnomad MID

AF:

0.0127

Gnomad NFE

AF:

0.00703

Gnomad OTH

AF:

0.00716

GnomAD3 exomes

AF:

0.00447

AC:

581

AN:

130020

Hom.:

AF XY:

0.00501

AC XY:

355

AN XY:

70832

show subpopulations

Gnomad AFR exome

AF:

0.000321

Gnomad AMR exome

AF:

0.00332

Gnomad ASJ exome

AF:

0.00185

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00585

Gnomad FIN exome

AF:

0.00260

Gnomad NFE exome

AF:

0.00614

Gnomad OTH exome

AF:

0.00919

GnomAD4 exome

AF:

0.00553

AC:

3030

AN:

548168

Hom.:

Cov.:

AF XY:

0.00571

AC XY:

1694

AN XY:

296748

show subpopulations

Gnomad4 AFR exome

AF:

0.00102

Gnomad4 AMR exome

AF:

0.00375

Gnomad4 ASJ exome

AF:

0.00170

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.00568

Gnomad4 FIN exome

AF:

0.00343

Gnomad4 NFE exome

AF:

0.00680

Gnomad4 OTH exome

AF:

0.00618

GnomAD4 genome

AF:

0.00438

AC:

668

AN:

152350

Hom.:

Cov.:

AF XY:

0.00420

AC XY:

313

AN XY:

74506

show subpopulations

Gnomad4 AFR

AF:

0.000962

Gnomad4 AMR

AF:

0.00503

Gnomad4 ASJ

AF:

0.00375

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00455

Gnomad4 FIN

AF:

0.00179

Gnomad4 NFE

AF:

0.00703

Gnomad4 OTH

AF:

0.00756

Alfa

AF:

0.00220

Hom.:

Bravo

AF:

0.00453

TwinsUK

AF:

0.00566

AC:

ALSPAC

AF:

0.00778

AC:

ExAC

AF:

0.00372

AC:

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

Apr 01, 2023

WDR97: PP2, BP4, BS2 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.13

BayesDel_addAF

Benign

-0.52

BayesDel_noAF

Benign

-0.51

CADD

Benign

1.9

DANN

Benign

0.86

DEOGEN2

Benign

0.0062

Eigen

Benign

-0.71

Eigen_PC

Benign

-0.90

FATHMM_MKL

Benign

0.053

LIST_S2

Benign

0.51

M_CAP

Benign

0.083

MetaRNN

Benign

0.0052

MetaSVM

Benign

-1.0

MutationTaster

Benign

1.0

PROVEAN

Benign

-0.32

REVEL

Benign

0.0080

Sift

Benign

0.26

Sift4G

Benign

0.19

Vest4

0.060

MVP

0.19

ClinPred

0.0091

GERP RS

-0.038

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.3

Varity_R

0.060

gMVP

0.73

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over