Menu
GeneBe

5-111097122-C-T

Variant summary

Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_ModerateBP6_Very_StrongBP7BS2

The NM_139281.3(WDR36):c.234C>T(p.Gly78=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0124 in 1,613,494 control chromosomes in the GnomAD database, including 188 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.0094 ( 24 hom., cov: 32)
Exomes 𝑓: 0.013 ( 164 hom. )

Consequence

WDR36
NM_139281.3 synonymous

Scores

2

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 0.655
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -15 ACMG points.

BP4
?
    BP4 - Multiple lines of computational evidence suggest no impact on gene or gene product (conservation, evolutionary, splicing impact, etc.)
Computational evidence support a benign effect (BayesDel_noAF=-0.32).
BP6
?
    BP6 - Reputable source recently reports variant as benign, but the evidence is not available to the laboratory to perform an independent evaluation
Variant 5-111097122-C-T is Benign according to our data. Variant chr5-111097122-C-T is described in ClinVar as [Benign]. Clinvar id is 1571445.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BP7
?
    BP7 - A synonymous (silent) variant for which splicing prediction algorithms predict no impact to the splice consensus sequence nor the creation of a new splice site AND the nucleotide is not highly conserved
Synonymous conserved (PhyloP=0.655 with no splicing effect.
BS2
?
    BS2 - Observed in a healthy adult individual for a recessive (homozygous), dominant (heterozygous), or X-linked (hemizygous) disorder, with full penetrance expected at an early age
High Homozygotes in GnomAd at 24 gene

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
WDR36NM_139281.3 linkuse as main transcriptc.234C>T p.Gly78= synonymous_variant 3/23 ENST00000513710.4
WDR36XM_047416729.1 linkuse as main transcriptc.234C>T p.Gly78= synonymous_variant 3/21

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
WDR36ENST00000513710.4 linkuse as main transcriptc.234C>T p.Gly78= synonymous_variant 3/231 NM_139281.3 P1
WDR36ENST00000504122.2 linkuse as main transcriptn.116C>T non_coding_transcript_exon_variant 1/54
WDR36ENST00000505303.5 linkuse as main transcriptn.370C>T non_coding_transcript_exon_variant 3/155

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.00940
AC:
1429
AN:
152066
Hom.:
24
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.00312
Gnomad AMI
AF:
0.184
Gnomad AMR
AF:
0.00662
Gnomad ASJ
AF:
0.00576
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00623
Gnomad FIN
AF:
0.00312
Gnomad MID
AF:
0.00316
Gnomad NFE
AF:
0.0137
Gnomad OTH
AF:
0.00909
GnomAD3 exomes
AF:
0.00992
AC:
2493
AN:
251256
Hom.:
17
AF XY:
0.0102
AC XY:
1383
AN XY:
135788
show subpopulations
Gnomad AFR exome
AF:
0.00277
Gnomad AMR exome
AF:
0.00720
Gnomad ASJ exome
AF:
0.00546
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.00676
Gnomad FIN exome
AF:
0.00379
Gnomad NFE exome
AF:
0.0158
Gnomad OTH exome
AF:
0.0103
GnomAD4 exome
AF:
0.0128
AC:
18652
AN:
1461310
Hom.:
164
Cov.:
30
AF XY:
0.0127
AC XY:
9207
AN XY:
726988
show subpopulations
Gnomad4 AFR exome
AF:
0.00290
Gnomad4 AMR exome
AF:
0.00733
Gnomad4 ASJ exome
AF:
0.00528
Gnomad4 EAS exome
AF:
0.0000505
Gnomad4 SAS exome
AF:
0.00734
Gnomad4 FIN exome
AF:
0.00397
Gnomad4 NFE exome
AF:
0.0149
Gnomad4 OTH exome
AF:
0.0104
GnomAD4 genome
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.00938
AC:
1428
AN:
152184
Hom.:
24
Cov.:
32
AF XY:
0.00891
AC XY:
663
AN XY:
74404
show subpopulations
Gnomad4 AFR
AF:
0.00311
Gnomad4 AMR
AF:
0.00661
Gnomad4 ASJ
AF:
0.00576
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00623
Gnomad4 FIN
AF:
0.00312
Gnomad4 NFE
AF:
0.0136
Gnomad4 OTH
AF:
0.00900
Alfa
AF:
0.0121
Hom.:
6
Bravo
AF:
0.00989
Asia WGS
AF:
0.00115
AC:
4
AN:
3476
EpiCase
AF:
0.0139
EpiControl
AF:
0.0138

ClinVar

Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link

Submissions by phenotype

WDR36-related disorder Benign:1
Benign, criteria provided, single submitterclinical testingPreventionGenetics, part of Exact SciencesJul 15, 2019This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
not provided Benign:1
Benign, criteria provided, single submitterclinical testingInvitaeJan 02, 2024- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.32
Cadd
Benign
8.4
Dann
Benign
0.68
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.7

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.

Other links and lift over

dbSNP: rs148990528; hg19: chr5-110432820; COSMIC: COSV101540832; COSMIC: COSV101540832; API