Variant 19-37885345-G-A 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.8326C>T(p.Arg2776Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00434 in 1,551,650 control chromosomes in the GnomAD database, including 225 homozygotes. In-silico tool predicts a benign outcome for this variant. 10/17 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. R2776Q) has been classified as Benign.

Frequency

Genomes: 𝑓 0.0070 ( 35 hom., cov: 32)

Exomes 𝑓: 0.0040 ( 190 hom. )

Consequence

WDR87
NM_001291088.2 missense

Scores

Clinical Significance

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

Conservation

PhyloP100: 0.992

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=0.0028811097).

BP6

Variant 19-37885345-G-A is Benign according to our data. Variant chr19-37885345-G-A is described in ClinVar as [Benign]. Clinvar id is 1248661.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0631 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.8326C>T	p.Arg2776Trp	missense_variant	6/6	ENST00000447313.7
LOC105372395	XR_935962.3 linkuse as main transcript	n.621+846G>A		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.8326C>T	p.Arg2776Trp	missense_variant	6/6	2	NM_001291088.2	A2
WDR87	ENST00000303868.5 linkuse as main transcript	c.8209C>T	p.Arg2737Trp	missense_variant	6/6	2		P2

Frequencies

GnomAD3 genomes

AF:

0.00701

AC:

1067

AN:

152106

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00167

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0371

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.0690

Gnomad SAS

AF:

0.00912

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.000132

Gnomad OTH

AF:

0.0101

GnomAD3 exomes

AF:

0.0190

AC:

2972

AN:

156566

Hom.:

126

AF XY:

0.0164

AC XY:

1359

AN XY:

82976

show subpopulations

Gnomad AFR exome

AF:

0.00165

Gnomad AMR exome

AF:

0.0731

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.0795

Gnomad SAS exome

AF:

0.00931

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.0000660

Gnomad OTH exome

AF:

0.0166

GnomAD4 exome

AF:

0.00404

AC:

5658

AN:

1399426

Hom.:

190

Cov.:

AF XY:

0.00389

AC XY:

2687

AN XY:

690228

show subpopulations

Gnomad4 AFR exome

AF:

0.000760

Gnomad4 AMR exome

AF:

0.0696

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.0576

Gnomad4 SAS exome

AF:

0.00765

Gnomad4 FIN exome

AF:

0.00

Gnomad4 NFE exome

AF:

0.0000677

Gnomad4 OTH exome

AF:

0.00710

GnomAD4 genome

AF:

0.00704

AC:

1071

AN:

152224

Hom.:

Cov.:

AF XY:

0.00795

AC XY:

592

AN XY:

74428

show subpopulations

Gnomad4 AFR

AF:

0.00166

Gnomad4 AMR

AF:

0.0372

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.0689

Gnomad4 SAS

AF:

0.00912

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.000132

Gnomad4 OTH

AF:

0.0109

Alfa

AF:

0.000826

Hom.:

Bravo

AF:

0.0121

TwinsUK

AF:

0.000270

AC:

ALSPAC

AF:

0.00

AC:

ExAC

AF:

0.00514

AC:

131

Asia WGS

AF:

0.0310

AC:

109

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	Labcorp Genetics (formerly Invitae), Labcorp	Jan 26, 2024	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Jul 06, 2018	- -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.16

BayesDel_addAF

Benign

-0.47

BayesDel_noAF

Benign

-0.38

CADD

Uncertain

DANN

Benign

0.97

Eigen

Uncertain

0.41

Eigen_PC

Uncertain

0.39

FATHMM_MKL

Benign

0.63

LIST_S2

Benign

0.72

T;.

MetaRNN

Benign

0.0029

T;T

MetaSVM

Benign

-1.1

MutationTaster

Benign

0.86

N;N

PrimateAI

Benign

0.39

PROVEAN

Uncertain

-3.9

D;D

REVEL

Benign

0.15

Sift

Uncertain

0.0010

D;D

Sift4G

Uncertain

0.0020

D;D

Polyphen

1.0

D;.

Vest4

0.48

ClinPred

0.051

GERP RS

3.8

gMVP

0.28

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