Variant 19-37885098-T-C 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.8573A>G(p.Gln2858Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00188 in 1,464,468 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/18 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.0019 ( 0 hom., cov: 31)

Exomes 𝑓: 0.0019 ( 2 hom. )

Consequence

WDR87
NM_001291088.2 missense

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 0.245

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=0.005478412).

BP6

Variant 19-37885098-T-C is Benign according to our data. Variant chr19-37885098-T-C is described in ClinVar as [Benign]. Clinvar id is 1599979.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BS2

High Homozygotes in GnomAdExome4 at 2 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
WDR87	NM_001291088.2 linkuse as main transcript	c.8573A>G	p.Gln2858Arg	missense_variant	6/6	ENST00000447313.7
LOC105372395	XR_935962.3 linkuse as main transcript	n.621+599T>C		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.8573A>G	p.Gln2858Arg	missense_variant	6/6	2	NM_001291088.2	A2
WDR87	ENST00000303868.5 linkuse as main transcript	c.8456A>G	p.Gln2819Arg	missense_variant	6/6	2		P2

Frequencies

GnomAD3 genomes

AF:

0.00188

AC:

286

AN:

152150

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000145

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.000917

Gnomad ASJ

AF:

0.0133

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.000622

Gnomad FIN

AF:

0.00433

Gnomad MID

AF:

0.00316

Gnomad NFE

AF:

0.00244

Gnomad OTH

AF:

0.00191

GnomAD3 exomes

AF:

0.00201

AC:

175

AN:

87158

Hom.:

AF XY:

0.00190

AC XY:

AN XY:

43152

show subpopulations

Gnomad AFR exome

AF:

0.000140

Gnomad AMR exome

AF:

0.000709

Gnomad ASJ exome

AF:

0.00840

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.000134

Gnomad FIN exome

AF:

0.00489

Gnomad NFE exome

AF:

0.00215

Gnomad OTH exome

AF:

0.00289

GnomAD4 exome

AF:

0.00188

AC:

2468

AN:

1312200

Hom.:

Cov.:

AF XY:

0.00191

AC XY:

1219

AN XY:

638262

show subpopulations

Gnomad4 AFR exome

AF:

0.0000701

Gnomad4 AMR exome

AF:

0.00112

Gnomad4 ASJ exome

AF:

0.00904

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.000445

Gnomad4 FIN exome

AF:

0.00576

Gnomad4 NFE exome

AF:

0.00176

Gnomad4 OTH exome

AF:

0.00234

GnomAD4 genome

AF:

0.00188

AC:

286

AN:

152268

Hom.:

Cov.:

AF XY:

0.00204

AC XY:

152

AN XY:

74466

show subpopulations

Gnomad4 AFR

AF:

0.000144

Gnomad4 AMR

AF:

0.000916

Gnomad4 ASJ

AF:

0.0133

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.000623

Gnomad4 FIN

AF:

0.00433

Gnomad4 NFE

AF:

0.00244

Gnomad4 OTH

AF:

0.00189

Alfa

AF:

0.00241

Hom.:

Bravo

AF:

0.00143

TwinsUK

AF:

0.00108

AC:

ALSPAC

AF:

0.00104

AC:

ESP6500AA

AF:

0.00

AC:

ESP6500EA

AF:

0.00189

AC:

ExAC

AF:

0.00167

AC:

Asia WGS

AF:

0.000577

AC:

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Oct 13, 2023	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.082

BayesDel_addAF

Benign

-0.68

BayesDel_noAF

Benign

-0.75

CADD

Benign

DANN

Benign

0.18

Eigen

Benign

-1.3

Eigen_PC

Benign

-1.4

FATHMM_MKL

Benign

0.017

LIST_S2

Benign

0.26

T;.

M_CAP

Benign

0.014

MetaRNN

Benign

0.0055

T;T

MetaSVM

Benign

-0.96

MutationTaster

Benign

1.0

N;N

PrimateAI

Benign

0.25

PROVEAN

Benign

-0.30

N;N

REVEL

Benign

0.0070

Sift

Benign

0.11

T;T

Sift4G

Benign

0.29

T;T

Polyphen

0.035

B;.

Vest4

0.091

MVP

0.030

ClinPred

0.0015

GERP RS

-2.5

gMVP

0.076

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