chr5-111121006-A-T

Variant names:

Variant summary

Our verdict is Benign. The variant received -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1

The NM_139281.3(WDR36):c.2013A>T(p.Val671Val) 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
NM_139281.3 synonymous

Scores

Clinical Significance

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

Conservation

PhyloP100: -0.955

Publications

21 publications found

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 Gene-Disease associations (from GenCC):

glaucoma 1, open angle, G
Inheritance: Unknown, AD Classification: LIMITED, NO_KNOWN Submitted by: Labcorp Genetics (formerly Invitae), ClinGen

WDR36 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -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 VariationId is 262465.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

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 rank	MANE	Protein	UniProt
WDR36	NM_139281.3 link	c.2013A>T	p.Val671Val	synonymous_variant	Exon 19 of 23	ENST00000513710.4	NP_644810.2	Q8NI36
WDR36	XM_047416729.1 link	c.2013A>T	p.Val671Val	synonymous_variant	Exon 19 of 21		XP_047272685.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
WDR36	ENST00000513710.4 link	c.2013A>T	p.Val671Val	synonymous_variant	Exon 19 of 23	1	NM_139281.3	ENSP00000424628.3		A0A0A0MTB8

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

GnomAD2 exomes

AF:

0.329

AC:

81934

AN:

249122

AF XY:

0.334

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 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

African (AFR)

AF:

0.0927

AC:

3100

AN:

33430

American (AMR)

AF:

0.412

AC:

18360

AN:

44532

Ashkenazi Jewish (ASJ)

AF:

0.391

AC:

10194

AN:

26052

East Asian (EAS)

AF:

0.244

AC:

9655

AN:

39590

South Asian (SAS)

AF:

0.402

AC:

34566

AN:

85940

European-Finnish (FIN)

AF:

0.392

AC:

20935

AN:

53378

Middle Eastern (MID)

AF:

0.400

AC:

2296

AN:

5744

European-Non Finnish (NFE)

AF:

0.306

AC:

339208

AN:

1109696

Other (OTH)

AF:

0.307

AC:

18519

AN:

60264

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.460

Heterozygous variant carriers

14871

29741

44612

59482

74353

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

11186

22372

33558

44744

55930

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.261

AC:

39669

AN:

152034

Hom.:

6073

Cov.:

AF XY:

0.268

AC XY:

19927

AN XY:

74314

show subpopulations

African (AFR)

AF:

0.100

AC:

4167

AN:

41538

American (AMR)

AF:

0.322

AC:

4908

AN:

15264

Ashkenazi Jewish (ASJ)

AF:

0.384

AC:

1332

AN:

3468

East Asian (EAS)

AF:

0.259

AC:

1340

AN:

5176

South Asian (SAS)

AF:

0.394

AC:

1899

AN:

4824

European-Finnish (FIN)

AF:

0.406

AC:

4287

AN:

10552

Middle Eastern (MID)

AF:

0.434

AC:

126

AN:

290

European-Non Finnish (NFE)

AF:

0.306

AC:

20785

AN:

67904

Other (OTH)

AF:

0.280

AC:

590

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1442

2884

4325

5767

7209

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

428

856

1284

1712

2140

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

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

Feb 03, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

May 10, 2018

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. -

not specified

Benign:1

PreventionGenetics, part of Exact Sciences

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Glaucoma 1, open angle, G

Benign:1

Dec 05, 2021

Genome-Nilou Lab

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.87

CADD

Benign

3.9

(source)

DANN

Benign

0.57

PhyloP100

-0.95

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

Other links and lift over