NM_139281.3:c.-95T>C
Variant names:
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
NM_139281.3 5_prime_UTR
Scores
16
Clinical Significance
Conservation
PhyloP100: -0.325
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]
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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
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
WDR36 | ENST00000513710 | c.-95T>C | 5_prime_UTR_variant | Exon 1 of 23 | 1 | NM_139281.3 | ENSP00000424628.3 | |||
WDR36 | ENST00000505303.5 | n.42T>C | non_coding_transcript_exon_variant | Exon 1 of 15 | 5 | |||||
WDR36 | ENST00000515784.1 | n.16T>C | non_coding_transcript_exon_variant | Exon 1 of 2 | 2 |
Frequencies
GnomAD3 genomes AF: 0.00752 AC: 1145AN: 152214Hom.: 3 Cov.: 33
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GnomAD3 exomes AF: 0.00724 AC: 1819AN: 251336Hom.: 15 AF XY: 0.00715 AC XY: 972AN XY: 135900
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GnomAD4 exome AF: 0.00945 AC: 13813AN: 1461882Hom.: 88 Cov.: 31 AF XY: 0.00912 AC XY: 6633AN XY: 727244
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GnomAD4 genome AF: 0.00752 AC: 1145AN: 152332Hom.: 3 Cov.: 33 AF XY: 0.00728 AC XY: 542AN XY: 74476
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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:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
DEOGEN2
Benign
T;T
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Benign
N
LIST_S2
Benign
.;T
MetaRNN
Benign
T;T
MetaSVM
Benign
T
MutationAssessor
Benign
N;N
PrimateAI
Benign
T
PROVEAN
Benign
N;.
REVEL
Benign
Polyphen
B;B
Vest4
MVP
MPC
ClinPred
T
GERP RS
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Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at