Variant 19-37885026-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_001291088.2(WDR87):c.8645G>A(p.Arg2882Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.178 in 1,435,868 control chromosomes in the GnomAD database, including 23,209 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/17 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R2882W) has been classified as Uncertain significance.

Frequency

Genomes: 𝑓 0.18 ( 2454 hom., cov: 31)

Exomes 𝑓: 0.18 ( 20755 hom. )

Consequence

WDR87
NM_001291088.2 missense

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:3

Conservation

PhyloP100: 0.952

Variant links:

Genes affected

WDR87 (HGNC:29934): (WD repeat domain 87)

WDR87 links:

LOC105372395 (HGNC:):

LOC105372395 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.0030496418).

BP6

Variant 19-37885026-C-T is Benign according to our data. Variant chr19-37885026-C-T is described in ClinVar as [Benign]. Clinvar id is 677199.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.194 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
WDR87	NM_001291088.2 linkuse as main transcript	c.8645G>A	p.Arg2882Gln	missense_variant	6/6	ENST00000447313.7
LOC105372395	XR_935962.3 linkuse as main transcript	n.621+527C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
WDR87	ENST00000447313.7 linkuse as main transcript	c.8645G>A	p.Arg2882Gln	missense_variant	6/6	2	NM_001291088.2	A2
WDR87	ENST00000303868.5 linkuse as main transcript	c.8528G>A	p.Arg2843Gln	missense_variant	6/6	2		P2

Frequencies

GnomAD3 genomes

AF:

0.179

AC:

27243

AN:

151876

Hom.:

2450

Cov.:

show subpopulations

Gnomad AFR

AF:

0.175

Gnomad AMI

AF:

0.264

Gnomad AMR

AF:

0.169

Gnomad ASJ

AF:

0.254

Gnomad EAS

AF:

0.123

Gnomad SAS

AF:

0.204

Gnomad FIN

AF:

0.207

Gnomad MID

AF:

0.294

Gnomad NFE

AF:

0.176

Gnomad OTH

AF:

0.196

GnomAD3 exomes

AF:

0.175

AC:

15170

AN:

86832

Hom.:

1427

AF XY:

0.176

AC XY:

7701

AN XY:

43830

show subpopulations

Gnomad AFR exome

AF:

0.168

Gnomad AMR exome

AF:

0.145

Gnomad ASJ exome

AF:

0.239

Gnomad EAS exome

AF:

0.110

Gnomad SAS exome

AF:

0.201

Gnomad FIN exome

AF:

0.208

Gnomad NFE exome

AF:

0.175

Gnomad OTH exome

AF:

0.176

GnomAD4 exome

AF:

0.178

AC:

228259

AN:

1283874

Hom.:

20755

Cov.:

AF XY:

0.179

AC XY:

111197

AN XY:

622294

show subpopulations

Gnomad4 AFR exome

AF:

0.172

Gnomad4 AMR exome

AF:

0.147

Gnomad4 ASJ exome

AF:

0.261

Gnomad4 EAS exome

AF:

0.115

Gnomad4 SAS exome

AF:

0.204

Gnomad4 FIN exome

AF:

0.197

Gnomad4 NFE exome

AF:

0.176

Gnomad4 OTH exome

AF:

0.189

GnomAD4 genome

AF:

0.179

AC:

27256

AN:

151994

Hom.:

2454

Cov.:

AF XY:

0.182

AC XY:

13544

AN XY:

74268

show subpopulations

Gnomad4 AFR

AF:

0.175

Gnomad4 AMR

AF:

0.168

Gnomad4 ASJ

AF:

0.254

Gnomad4 EAS

AF:

0.123

Gnomad4 SAS

AF:

0.205

Gnomad4 FIN

AF:

0.207

Gnomad4 NFE

AF:

0.176

Gnomad4 OTH

AF:

0.198

Alfa

AF:

0.176

Hom.:

3381

Bravo

AF:

0.176

TwinsUK

AF:

0.179

AC:

665

ALSPAC

AF:

0.168

AC:

648

ESP6500AA

AF:

0.182

AC:

252

ESP6500EA

AF:

0.173

AC:

550

ExAC

AF:

0.156

AC:

3881

Asia WGS

AF:

0.167

AC:

579

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:3

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:3

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Jan 26, 2024	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Mar 24, 2018	This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.077

BayesDel_addAF

Benign

-0.82

BayesDel_noAF

Benign

-0.81

CADD

Benign

DANN

Benign

0.78

Eigen

Benign

-1.1

Eigen_PC

Benign

-0.86

FATHMM_MKL

Benign

0.018

LIST_S2

Benign

0.56

T;.

MetaRNN

Benign

0.0030

T;T

MetaSVM

Benign

-0.93

MutationTaster

Benign

1.0

P;P

PrimateAI

Benign

0.19

PROVEAN

Benign

0.98

N;N

REVEL

Benign

0.023

Sift

Benign

1.0

T;T

Sift4G

Benign

1.0

T;T

Polyphen

0.0010

B;.

Vest4

0.013

ClinPred

0.0081

GERP RS

2.5

gMVP

0.025

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