Variant 5-111100751-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The NM_139281.3(WDR36):c.542+30C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.483 in 1,592,830 control chromosomes in the GnomAD database, including 191,876 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.54 ( 23196 hom., cov: 31)

Exomes 𝑓: 0.48 ( 168680 hom. )

Consequence

WDR36
NM_139281.3 intron

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.149

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:

WDR36 (HGNC:):

WDR36 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.79).

BP6

Variant 5-111100751-C-T is Benign according to our data. Variant chr5-111100751-C-T is described in ClinVar as [Benign]. Clinvar id is 1684227.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.678 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.542+30C>T		intron_variant		ENST00000513710.4	NP_644810.2	Q8NI36
WDR36	XM_047416729.1 linkuse as main transcript	c.542+30C>T		intron_variant			XP_047272685.1

Ensembl

Gene	Transcript	HGVSc	Effect	TSL	MANE	Protein	UniProt
WDR36	ENST00000513710.4 linkuse as main transcript	c.542+30C>T	intron_variant	1	NM_139281.3	ENSP00000424628.3	A0A0A0MTB8
WDR36	ENST00000504122.2 linkuse as main transcript	n.424+30C>T	intron_variant	4
WDR36	ENST00000505303.5 linkuse as main transcript	n.678+30C>T	intron_variant	5

Frequencies

GnomAD3 genomes

AF:

0.542

AC:

82101

AN:

151426

Hom.:

23157

Cov.:

show subpopulations

Gnomad AFR

AF:

0.685

Gnomad AMI

AF:

0.369

Gnomad AMR

AF:

0.547

Gnomad ASJ

AF:

0.493

Gnomad EAS

AF:

0.395

Gnomad SAS

AF:

0.685

Gnomad FIN

AF:

0.550

Gnomad MID

AF:

0.639

Gnomad NFE

AF:

0.459

Gnomad OTH

AF:

0.531

GnomAD3 exomes

AF:

0.527

AC:

129946

AN:

246684

Hom.:

35737

AF XY:

0.526

AC XY:

70246

AN XY:

133484

show subpopulations

Gnomad AFR exome

AF:

0.684

Gnomad AMR exome

AF:

0.639

Gnomad ASJ exome

AF:

0.494

Gnomad EAS exome

AF:

0.394

Gnomad SAS exome

AF:

0.685

Gnomad FIN exome

AF:

0.530

Gnomad NFE exome

AF:

0.453

Gnomad OTH exome

AF:

0.500

GnomAD4 exome

AF:

0.476

AC:

686480

AN:

1441286

Hom.:

168680

Cov.:

AF XY:

0.482

AC XY:

345768

AN XY:

717484

show subpopulations

Gnomad4 AFR exome

AF:

0.692

Gnomad4 AMR exome

AF:

0.630

Gnomad4 ASJ exome

AF:

0.495

Gnomad4 EAS exome

AF:

0.362

Gnomad4 SAS exome

AF:

0.682

Gnomad4 FIN exome

AF:

0.527

Gnomad4 NFE exome

AF:

0.448

Gnomad4 OTH exome

AF:

0.491

GnomAD4 genome

AF:

0.542

AC:

82199

AN:

151544

Hom.:

23196

Cov.:

AF XY:

0.548

AC XY:

40577

AN XY:

74068

show subpopulations

Gnomad4 AFR

AF:

0.685

Gnomad4 AMR

AF:

0.547

Gnomad4 ASJ

AF:

0.493

Gnomad4 EAS

AF:

0.396

Gnomad4 SAS

AF:

0.686

Gnomad4 FIN

AF:

0.550

Gnomad4 NFE

AF:

0.459

Gnomad4 OTH

AF:

0.530

Alfa

AF:

0.477

Hom.:

18462

Bravo

AF:

0.541

Asia WGS

AF:

0.540

AC:

1871

AN:

3462

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

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

-0.79

CADD

Benign

3.6

DANN

Benign

0.76

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