Variant chr5-111121006-A-T 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 ENST00000513710.4(WDR36):c.2013A>T(p.Val671=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.308 in 1,610,660 control chromosomes in the GnomAD database, including 80,231 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.26 ( 6073 hom., cov: 32)

Exomes 𝑓: 0.31 ( 74158 hom. )

Consequence

WDR36
ENST00000513710.4 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:4

Conservation

PhyloP100: -0.955

Variant links:

Genes affected

WDR36 (HGNC:30696): (WD repeat domain 36) This gene encodes a member of the WD repeat protein family. WD repeats are minimally conserved regions of approximately 40 amino acids typically bracketed by gly-his and trp-asp (GH-WD), which may facilitate formation of heterotrimeric or multiprotein complexes. Members of this family are involved in a variety of cellular processes, including cell cycle progression, signal transduction, apoptosis, and gene regulation. Mutations in this gene have been associated with adult-onset primary open-angle glaucoma (POAG). [provided by RefSeq, Jul 2008]

WDR36 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.87).

BP6

Variant 5-111121006-A-T is Benign according to our data. Variant chr5-111121006-A-T is described in ClinVar as [Benign]. Clinvar id is 262465.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr5-111121006-A-T is described in Lovd as [Benign].

BP7

Synonymous conserved (PhyloP=-0.955 with no splicing effect.

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.379 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
WDR36	NM_139281.3 linkuse as main transcript	c.2013A>T	p.Val671=	synonymous_variant	19/23	ENST00000513710.4	NP_644810.2
WDR36	XM_047416729.1 linkuse as main transcript	c.2013A>T	p.Val671=	synonymous_variant	19/21		XP_047272685.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
WDR36	ENST00000513710.4 linkuse as main transcript	c.2013A>T	p.Val671=	synonymous_variant	19/23	1	NM_139281.3	ENSP00000424628	P1

Frequencies

GnomAD3 genomes

AF:

0.261

AC:

39686

AN:

151916

Hom.:

6077

Cov.:

show subpopulations

Gnomad AFR

AF:

0.101

Gnomad AMI

AF:

0.258

Gnomad AMR

AF:

0.322

Gnomad ASJ

AF:

0.384

Gnomad EAS

AF:

0.258

Gnomad SAS

AF:

0.394

Gnomad FIN

AF:

0.406

Gnomad MID

AF:

0.423

Gnomad NFE

AF:

0.306

Gnomad OTH

AF:

0.284

GnomAD3 exomes

AF:

0.329

AC:

81934

AN:

249122

Hom.:

14551

AF XY:

0.334

AC XY:

45032

AN XY:

134900

show subpopulations

Gnomad AFR exome

AF:

0.0968

Gnomad AMR exome

AF:

0.425

Gnomad ASJ exome

AF:

0.391

Gnomad EAS exome

AF:

0.247

Gnomad SAS exome

AF:

0.406

Gnomad FIN exome

AF:

0.395

Gnomad NFE exome

AF:

0.306

Gnomad OTH exome

AF:

0.330

GnomAD4 exome

AF:

0.313

AC:

456833

AN:

1458626

Hom.:

74158

Cov.:

AF XY:

0.317

AC XY:

230081

AN XY:

725656

show subpopulations

Gnomad4 AFR exome

AF:

0.0927

Gnomad4 AMR exome

AF:

0.412

Gnomad4 ASJ exome

AF:

0.391

Gnomad4 EAS exome

AF:

0.244

Gnomad4 SAS exome

AF:

0.402

Gnomad4 FIN exome

AF:

0.392

Gnomad4 NFE exome

AF:

0.306

Gnomad4 OTH exome

AF:

0.307

GnomAD4 genome

AF:

0.261

AC:

39669

AN:

152034

Hom.:

6073

Cov.:

AF XY:

0.268

AC XY:

19927

AN XY:

74314

show subpopulations

Gnomad4 AFR

AF:

0.100

Gnomad4 AMR

AF:

0.322

Gnomad4 ASJ

AF:

0.384

Gnomad4 EAS

AF:

0.259

Gnomad4 SAS

AF:

0.394

Gnomad4 FIN

AF:

0.406

Gnomad4 NFE

AF:

0.306

Gnomad4 OTH

AF:

0.280

Alfa

AF:

0.299

Hom.:

2342

Bravo

AF:

0.248

Asia WGS

AF:

0.296

AC:

1029

AN:

3476

EpiCase

AF:

0.322

EpiControl

AF:

0.316

ClinVar

Significance: Benign

Submissions summary: Benign:4

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	clinical testing	GeneDx	May 10, 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. -
Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Jan 31, 2024	- -

not specified

Benign:1

Benign, criteria provided, single submitter

clinical testing

PreventionGenetics, part of Exact Sciences

- -

Glaucoma 1, open angle, G

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

-0.87

CADD

Benign

3.9

DANN

Benign

0.57

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.040

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