Variant chr19-37885190-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1

The NM_001291088.2(WDR87):c.8481C>T(p.Tyr2827=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0457 in 1,474,988 control chromosomes in the GnomAD database, including 1,774 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.054 ( 254 hom., cov: 32)

Exomes 𝑓: 0.045 ( 1520 hom. )

Consequence

WDR87
NM_001291088.2 synonymous

Scores

Clinical Significance

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

Conservation

PhyloP100: 0.456

Variant links:

Genes affected

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

WDR87 links:

LOC105372395 (HGNC:):

LOC105372395 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.89).

BP6

Variant 19-37885190-G-A is Benign according to our data. Variant chr19-37885190-G-A is described in ClinVar as [Benign]. Clinvar id is 1280591.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=0.456 with no splicing effect.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.095 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.8481C>T	p.Tyr2827=	synonymous_variant	6/6	ENST00000447313.7
LOC105372395	XR_935962.3 linkuse as main transcript	n.621+691G>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.8481C>T	p.Tyr2827=	synonymous_variant	6/6	2	NM_001291088.2	A2
WDR87	ENST00000303868.5 linkuse as main transcript	c.8364C>T	p.Tyr2788=	synonymous_variant	6/6	2		P2

Frequencies

GnomAD3 genomes

AF:

0.0541

AC:

8224

AN:

152090

Hom.:

253

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0713

Gnomad AMI

AF:

0.00329

Gnomad AMR

AF:

0.0743

Gnomad ASJ

AF:

0.0294

Gnomad EAS

AF:

0.102

Gnomad SAS

AF:

0.0303

Gnomad FIN

AF:

0.0539

Gnomad MID

AF:

0.0190

Gnomad NFE

AF:

0.0394

Gnomad OTH

AF:

0.0475

GnomAD3 exomes

AF:

0.0539

AC:

4951

AN:

91886

Hom.:

163

AF XY:

0.0512

AC XY:

2342

AN XY:

45702

show subpopulations

Gnomad AFR exome

AF:

0.0650

Gnomad AMR exome

AF:

0.0726

Gnomad ASJ exome

AF:

0.0381

Gnomad EAS exome

AF:

0.110

Gnomad SAS exome

AF:

0.0302

Gnomad FIN exome

AF:

0.0469

Gnomad NFE exome

AF:

0.0414

Gnomad OTH exome

AF:

0.0569

GnomAD4 exome

AF:

0.0448

AC:

59207

AN:

1322780

Hom.:

1520

Cov.:

AF XY:

0.0446

AC XY:

28783

AN XY:

645242

show subpopulations

Gnomad4 AFR exome

AF:

0.0676

Gnomad4 AMR exome

AF:

0.0755

Gnomad4 ASJ exome

AF:

0.0350

Gnomad4 EAS exome

AF:

0.105

Gnomad4 SAS exome

AF:

0.0330

Gnomad4 FIN exome

AF:

0.0514

Gnomad4 NFE exome

AF:

0.0417

Gnomad4 OTH exome

AF:

0.0530

GnomAD4 genome

AF:

0.0541

AC:

8232

AN:

152208

Hom.:

254

Cov.:

AF XY:

0.0541

AC XY:

4025

AN XY:

74432

show subpopulations

Gnomad4 AFR

AF:

0.0711

Gnomad4 AMR

AF:

0.0748

Gnomad4 ASJ

AF:

0.0294

Gnomad4 EAS

AF:

0.102

Gnomad4 SAS

AF:

0.0301

Gnomad4 FIN

AF:

0.0539

Gnomad4 NFE

AF:

0.0394

Gnomad4 OTH

AF:

0.0479

Alfa

AF:

0.0436

Hom.:

Bravo

AF:

0.0584

Asia WGS

AF:

0.0750

AC:

260

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	Jul 09, 2018	- -
Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Jan 26, 2024	- -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

7.0

DANN

Benign

0.17

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