Variant chr19-36091368-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_001083961.2(WDR62):c.2147-34G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.53 in 1,356,602 control chromosomes in the GnomAD database, including 163,932 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.42 ( 13623 hom., cov: 31)

Exomes 𝑓: 0.54 ( 150309 hom. )

Consequence

WDR62
NM_001083961.2 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:5

Conservation

PhyloP100: 1.16

Variant links:

Genes affected

WDR62 (HGNC:24502): (WD repeat domain 62) This gene is proposed to play a role in cerebral cortical development. Mutations in this gene have been associated with microencephaly, cortical malformations, and cognitive disability. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jan 2011]

WDR62 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 (BayesDel_noAF=-0.81).

BP6

Variant 19-36091368-G-A is Benign according to our data. Variant chr19-36091368-G-A is described in ClinVar as [Benign]. Clinvar id is 160261.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.57 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
WDR62	NM_001083961.2 linkuse as main transcript	c.2147-34G>A		intron_variant		ENST00000401500.7	NP_001077430.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
WDR62	ENST00000401500.7 linkuse as main transcript	c.2147-34G>A		intron_variant		1	NM_001083961.2	ENSP00000384792	P4	O43379-4

Frequencies

GnomAD3 genomes

AF:

0.424

AC:

62758

AN:

147900

Hom.:

13612

Cov.:

show subpopulations

Gnomad AFR

AF:

0.301

Gnomad AMI

AF:

0.277

Gnomad AMR

AF:

0.507

Gnomad ASJ

AF:

0.371

Gnomad EAS

AF:

0.589

Gnomad SAS

AF:

0.319

Gnomad FIN

AF:

0.528

Gnomad MID

AF:

0.334

Gnomad NFE

AF:

0.465

Gnomad OTH

AF:

0.414

GnomAD3 exomes

AF:

0.444

AC:

111328

AN:

250824

Hom.:

25751

AF XY:

0.434

AC XY:

58776

AN XY:

135584

show subpopulations

Gnomad AFR exome

AF:

0.289

Gnomad AMR exome

AF:

0.571

Gnomad ASJ exome

AF:

0.376

Gnomad EAS exome

AF:

0.555

Gnomad SAS exome

AF:

0.286

Gnomad FIN exome

AF:

0.489

Gnomad NFE exome

AF:

0.450

Gnomad OTH exome

AF:

0.429

GnomAD4 exome

AF:

0.543

AC:

656258

AN:

1208572

Hom.:

150309

Cov.:

AF XY:

0.532

AC XY:

322784

AN XY:

607000

show subpopulations

Gnomad4 AFR exome

AF:

0.398

Gnomad4 AMR exome

AF:

0.588

Gnomad4 ASJ exome

AF:

0.459

Gnomad4 EAS exome

AF:

0.653

Gnomad4 SAS exome

AF:

0.317

Gnomad4 FIN exome

AF:

0.544

Gnomad4 NFE exome

AF:

0.564

Gnomad4 OTH exome

AF:

0.528

GnomAD4 genome

AF:

0.424

AC:

62794

AN:

148030

Hom.:

13623

Cov.:

AF XY:

0.427

AC XY:

30805

AN XY:

72160

show subpopulations

Gnomad4 AFR

AF:

0.301

Gnomad4 AMR

AF:

0.508

Gnomad4 ASJ

AF:

0.371

Gnomad4 EAS

AF:

0.588

Gnomad4 SAS

AF:

0.317

Gnomad4 FIN

AF:

0.528

Gnomad4 NFE

AF:

0.465

Gnomad4 OTH

AF:

0.414

Alfa

AF:

0.427

Hom.:

3677

Bravo

AF:

0.413

Asia WGS

AF:

0.386

AC:

1340

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:5

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:2

Likely benign, no assertion criteria provided	clinical testing	Genetic Services Laboratory, University of Chicago	-	- -
Benign, criteria provided, single submitter	clinical testing	PreventionGenetics, part of Exact Sciences	-	- -

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Jun 19, 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. -

Microcephaly 2, primary, autosomal recessive, with or without cortical malformations

Benign:1

Benign, criteria provided, single submitter

clinical testing

Genome-Nilou Lab

Dec 05, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.81

CADD

Benign

7.3

DANN

Benign

0.57

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.020

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