chr5-111092362-T-C

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2

The NM_139281.3(WDR36):​c.-95T>C variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00927 in 1,614,214 control chromosomes in the GnomAD database, including 91 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.0075 ( 3 hom., cov: 33)
Exomes 𝑓: 0.0094 ( 88 hom. )

Consequence

WDR36
NM_139281.3 5_prime_UTR

Scores

16

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.325
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 -10 ACMG points.

BP4
Computational evidence support a benign effect (MetaRNN=0.0030579567).
BP6
Variant 5-111092362-T-C is Benign according to our data. Variant chr5-111092362-T-C is described in ClinVar as [Benign]. Clinvar id is 350297.Status of the report is criteria_provided_single_submitter, 1 stars.
BS2
High Homozygotes in GnomAd4 at 3 gene

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
WDR36NM_139281.3 linkc.-95T>C 5_prime_UTR_variant Exon 1 of 23 ENST00000513710.4 NP_644810.2 Q8NI36
WDR36XM_047416729.1 linkc.-95T>C 5_prime_UTR_variant Exon 1 of 21 XP_047272685.1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
WDR36ENST00000513710 linkc.-95T>C 5_prime_UTR_variant Exon 1 of 23 1 NM_139281.3 ENSP00000424628.3 A0A0A0MTB8
WDR36ENST00000505303.5 linkn.42T>C non_coding_transcript_exon_variant Exon 1 of 15 5
WDR36ENST00000515784.1 linkn.16T>C non_coding_transcript_exon_variant Exon 1 of 2 2

Frequencies

GnomAD3 genomes
AF:
0.00752
AC:
1145
AN:
152214
Hom.:
3
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.00275
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.0126
Gnomad ASJ
AF:
0.0343
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.000413
Gnomad FIN
AF:
0.000847
Gnomad MID
AF:
0.00316
Gnomad NFE
AF:
0.00999
Gnomad OTH
AF:
0.0129
GnomAD3 exomes
AF:
0.00724
AC:
1819
AN:
251336
Hom.:
15
AF XY:
0.00715
AC XY:
972
AN XY:
135900
show subpopulations
Gnomad AFR exome
AF:
0.00210
Gnomad AMR exome
AF:
0.00755
Gnomad ASJ exome
AF:
0.0309
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.0000980
Gnomad FIN exome
AF:
0.000878
Gnomad NFE exome
AF:
0.00990
Gnomad OTH exome
AF:
0.0108
GnomAD4 exome
AF:
0.00945
AC:
13813
AN:
1461882
Hom.:
88
Cov.:
31
AF XY:
0.00912
AC XY:
6633
AN XY:
727244
show subpopulations
Gnomad4 AFR exome
AF:
0.00155
Gnomad4 AMR exome
AF:
0.00881
Gnomad4 ASJ exome
AF:
0.0332
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.0000812
Gnomad4 FIN exome
AF:
0.00114
Gnomad4 NFE exome
AF:
0.0107
Gnomad4 OTH exome
AF:
0.00886
GnomAD4 genome
AF:
0.00752
AC:
1145
AN:
152332
Hom.:
3
Cov.:
33
AF XY:
0.00728
AC XY:
542
AN XY:
74476
show subpopulations
Gnomad4 AFR
AF:
0.00274
Gnomad4 AMR
AF:
0.0126
Gnomad4 ASJ
AF:
0.0343
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.000414
Gnomad4 FIN
AF:
0.000847
Gnomad4 NFE
AF:
0.00999
Gnomad4 OTH
AF:
0.0128
Alfa
AF:
0.0108
Hom.:
15
Bravo
AF:
0.00859
TwinsUK
AF:
0.0102
AC:
38
ALSPAC
AF:
0.0112
AC:
43
ESP6500AA
AF:
0.00341
AC:
15
ESP6500EA
AF:
0.0116
AC:
100
ExAC
AF:
0.00654
AC:
794
Asia WGS
AF:
0.00115
AC:
4
AN:
3478
EpiCase
AF:
0.0105
EpiControl
AF:
0.0127

ClinVar

Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not provided Benign:1
Nov 01, 2024
Labcorp Genetics (formerly Invitae), Labcorp
Significance: Benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing

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Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.081
BayesDel_addAF
Benign
-0.61
T
BayesDel_noAF
Benign
-0.64
CADD
Benign
2.4
DANN
Benign
0.61
DEOGEN2
Benign
0.074
T;T
Eigen
Benign
-1.2
Eigen_PC
Benign
-1.3
FATHMM_MKL
Benign
0.12
N
LIST_S2
Benign
0.19
.;T
MetaRNN
Benign
0.0031
T;T
MetaSVM
Benign
-1.0
T
MutationAssessor
Benign
0.0
N;N
PrimateAI
Benign
0.36
T
PROVEAN
Benign
0.18
N;.
REVEL
Benign
0.098
Polyphen
0.0
B;B
Vest4
0.062
MVP
0.13
MPC
0.037
ClinPred
0.0054
T
GERP RS
-4.7
Varity_R
0.32
gMVP
0.19

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: rs145437203; hg19: chr5-110428060; COSMIC: COSV72411277; COSMIC: COSV72411277; API