Variant chr19-37885344-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP4_StrongBP6_Very_StrongBS2

The NM_001291088.2(WDR87):c.8327G>A(p.Arg2776Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0072 in 1,551,678 control chromosomes in the GnomAD database, including 62 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/18 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.0039 ( 1 hom., cov: 32)

Exomes 𝑓: 0.0076 ( 61 hom. )

Consequence

WDR87
NM_001291088.2 missense

Scores

Clinical Significance

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

Conservation

PhyloP100: 0.979

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 -16 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.006880492).

BP6

Variant 19-37885344-C-T is Benign according to our data. Variant chr19-37885344-C-T is described in ClinVar as [Benign]. Clinvar id is 1287795.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BS2

High Homozygotes in GnomAdExome4 at 61 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
WDR87	NM_001291088.2 linkuse as main transcript	c.8327G>A	p.Arg2776Gln	missense_variant	6/6	ENST00000447313.7	NP_001278017.1	E7ESW6B4DZG8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
WDR87	ENST00000447313.7 linkuse as main transcript	c.8327G>A	p.Arg2776Gln	missense_variant	6/6	2	NM_001291088.2	ENSP00000405012.2		E7ESW6
WDR87	ENST00000303868.5 linkuse as main transcript	c.8210G>A	p.Arg2737Gln	missense_variant	6/6	2		ENSP00000368025.3		Q6ZQQ6

Frequencies

GnomAD3 genomes

AF:

0.00390

AC:

594

AN:

152130

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00152

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.000720

Gnomad ASJ

AF:

0.00173

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.000471

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00741

Gnomad OTH

AF:

0.00239

GnomAD3 exomes

AF:

0.00355

AC:

556

AN:

156620

Hom.:

AF XY:

0.00338

AC XY:

281

AN XY:

83014

show subpopulations

Gnomad AFR exome

AF:

0.00152

Gnomad AMR exome

AF:

0.000851

Gnomad ASJ exome

AF:

0.00200

Gnomad EAS exome

AF:

0.0000918

Gnomad SAS exome

AF:

0.000132

Gnomad FIN exome

AF:

0.00119

Gnomad NFE exome

AF:

0.00770

Gnomad OTH exome

AF:

0.00342

GnomAD4 exome

AF:

0.00756

AC:

10580

AN:

1399430

Hom.:

Cov.:

AF XY:

0.00731

AC XY:

5043

AN XY:

690218

show subpopulations

Gnomad4 AFR exome

AF:

0.00139

Gnomad4 AMR exome

AF:

0.000728

Gnomad4 ASJ exome

AF:

0.00203

Gnomad4 EAS exome

AF:

0.0000839

Gnomad4 SAS exome

AF:

0.000151

Gnomad4 FIN exome

AF:

0.00126

Gnomad4 NFE exome

AF:

0.00936

Gnomad4 OTH exome

AF:

0.00477

GnomAD4 genome

AF:

0.00390

AC:

594

AN:

152248

Hom.:

Cov.:

AF XY:

0.00361

AC XY:

269

AN XY:

74430

show subpopulations

Gnomad4 AFR

AF:

0.00152

Gnomad4 AMR

AF:

0.000720

Gnomad4 ASJ

AF:

0.00173

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00

Gnomad4 FIN

AF:

0.000471

Gnomad4 NFE

AF:

0.00741

Gnomad4 OTH

AF:

0.00237

Alfa

AF:

0.00640

Hom.:

Bravo

AF:

0.00406

TwinsUK

AF:

0.00917

AC:

ALSPAC

AF:

0.0138

AC:

ESP6500AA

AF:

0.00289

AC:

ESP6500EA

AF:

0.00817

AC:

ExAC

AF:

0.00262

AC:

Asia WGS

AF:

0.000289

AC:

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	clinical testing	GeneDx	Jun 23, 2021	This variant is associated with the following publications: (PMID: 27535533) -
Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Jan 26, 2024	- -
Benign, criteria provided, single submitter	clinical testing	CeGaT Center for Human Genetics Tuebingen	Jan 01, 2023	WDR87: PP2, BP4, BS1, BS2 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.10

BayesDel_addAF

Benign

-0.50

BayesDel_noAF

Benign

-0.48

CADD

Benign

DANN

Benign

0.97

Eigen

Uncertain

0.25

Eigen_PC

Benign

0.22

FATHMM_MKL

Benign

0.60

LIST_S2

Benign

0.61

T;.

M_CAP

Benign

0.044

MetaRNN

Benign

0.0069

T;T

MetaSVM

Benign

-1.1

PrimateAI

Benign

0.31

PROVEAN

Benign

-1.7

N;N

REVEL

Benign

0.086

Sift

Benign

0.077

T;T

Sift4G

Benign

0.066

T;T

Polyphen

1.0

D;.

Vest4

0.26

MVP

0.25

ClinPred

0.038

GERP RS

2.6

gMVP

0.15

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.14

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