Variant NM_001083961.2:c.700-18C>T 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.700-18C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.302 in 1,612,366 control chromosomes in the GnomAD database, including 75,105 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.28 ( 6431 hom., cov: 33)

Exomes 𝑓: 0.30 ( 68674 hom. )

Consequence

WDR62
NM_001083961.2 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:9

Conservation

PhyloP100: 0.403

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=-0.82).

BP6

Variant 19-36067810-C-T is Benign according to our data. Variant chr19-36067810-C-T is described in ClinVar as [Benign]. Clinvar id is 137906.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr19-36067810-C-T is described in Lovd as [Benign].

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.322 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
WDR62	NM_001083961.2 link	c.700-18C>T		intron_variant	Intron 6 of 31	ENST00000401500.7	NP_001077430.1	O43379-4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
WDR62	ENST00000401500.7 link	c.700-18C>T		intron_variant	Intron 6 of 31	1	NM_001083961.2	ENSP00000384792.1		O43379-4

Frequencies

GnomAD3 genomes

AF:

0.284

AC:

43251

AN:

152052

Hom.:

6434

Cov.:

show subpopulations

Gnomad AFR

AF:

0.226

Gnomad AMI

AF:

0.148

Gnomad AMR

AF:

0.268

Gnomad ASJ

AF:

0.289

Gnomad EAS

AF:

0.267

Gnomad SAS

AF:

0.181

Gnomad FIN

AF:

0.340

Gnomad MID

AF:

0.266

Gnomad NFE

AF:

0.325

Gnomad OTH

AF:

0.285

GnomAD3 exomes

AF:

0.281

AC:

70000

AN:

249524

Hom.:

10076

AF XY:

0.280

AC XY:

37760

AN XY:

135054

show subpopulations

Gnomad AFR exome

AF:

0.229

Gnomad AMR exome

AF:

0.237

Gnomad ASJ exome

AF:

0.291

Gnomad EAS exome

AF:

0.268

Gnomad SAS exome

AF:

0.181

Gnomad FIN exome

AF:

0.330

Gnomad NFE exome

AF:

0.320

Gnomad OTH exome

AF:

0.282

GnomAD4 exome

AF:

0.304

AC:

443509

AN:

1460198

Hom.:

68674

Cov.:

AF XY:

0.301

AC XY:

218457

AN XY:

726472

show subpopulations

Gnomad4 AFR exome

AF:

0.228

Gnomad4 AMR exome

AF:

0.236

Gnomad4 ASJ exome

AF:

0.288

Gnomad4 EAS exome

AF:

0.290

Gnomad4 SAS exome

AF:

0.185

Gnomad4 FIN exome

AF:

0.333

Gnomad4 NFE exome

AF:

0.319

Gnomad4 OTH exome

AF:

0.285

GnomAD4 genome

AF:

0.284

AC:

43266

AN:

152168

Hom.:

6431

Cov.:

AF XY:

0.283

AC XY:

21021

AN XY:

74394

show subpopulations

Gnomad4 AFR

AF:

0.226

Gnomad4 AMR

AF:

0.268

Gnomad4 ASJ

AF:

0.289

Gnomad4 EAS

AF:

0.266

Gnomad4 SAS

AF:

0.180

Gnomad4 FIN

AF:

0.340

Gnomad4 NFE

AF:

0.325

Gnomad4 OTH

AF:

0.284

Alfa

AF:

0.304

Hom.:

1186

Bravo

AF:

0.275

Asia WGS

AF:

0.204

AC:

708

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:9

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:4

PreventionGenetics, part of Exact Sciences

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Dec 18, 2013

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

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. -

Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+

Significance: Benign

Review Status: no assertion criteria provided

Collection Method: clinical testing

- -

Genetic Services Laboratory, University of Chicago

Significance: Likely benign

Review Status: no assertion criteria provided

Collection Method: clinical testing

- -

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

Benign:3

Sep 21, 2015

Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen

Significance: Benign

Review Status: no assertion criteria provided

Collection Method: clinical testing

- -

Dec 05, 2021

Genome-Nilou Lab

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

not provided

Benign:2

Feb 03, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Breakthrough Genomics, Breakthrough Genomics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: not provided

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.82

CADD

Benign

9.9

DANN

Benign

0.74

RBP_binding_hub_radar

0.67

RBP_regulation_power_radar

1.8

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