5-111097143-T-C
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_139281.3(WDR36):c.255T>C(p.Tyr85=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0079 in 1,613,718 control chromosomes in the GnomAD database, including 868 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.042 ( 448 hom., cov: 32)
Exomes 𝑓: 0.0044 ( 420 hom. )
Consequence
WDR36
NM_139281.3 synonymous
NM_139281.3 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.681
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 -20 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.55).
BP6
?
Variant 5-111097143-T-C is Benign according to our data. Variant chr5-111097143-T-C is described in ClinVar as [Benign]. Clinvar id is 1260106.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.142 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
WDR36 | NM_139281.3 | c.255T>C | p.Tyr85= | synonymous_variant | 3/23 | ENST00000513710.4 | |
WDR36 | XM_047416729.1 | c.255T>C | p.Tyr85= | synonymous_variant | 3/21 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
WDR36 | ENST00000513710.4 | c.255T>C | p.Tyr85= | synonymous_variant | 3/23 | 1 | NM_139281.3 | P1 | |
WDR36 | ENST00000504122.2 | n.137T>C | non_coding_transcript_exon_variant | 1/5 | 4 | ||||
WDR36 | ENST00000505303.5 | n.391T>C | non_coding_transcript_exon_variant | 3/15 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.0417 AC: 6348AN: 152166Hom.: 448 Cov.: 32
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GnomAD3 exomes AF: 0.0108 AC: 2713AN: 251256Hom.: 188 AF XY: 0.00789 AC XY: 1071AN XY: 135792
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GnomAD4 exome AF: 0.00437 AC: 6381AN: 1461434Hom.: 420 Cov.: 30 AF XY: 0.00388 AC XY: 2822AN XY: 727034
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GnomAD4 genome ? AF: 0.0418 AC: 6364AN: 152284Hom.: 448 Cov.: 32 AF XY: 0.0407 AC XY: 3032AN XY: 74478
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ClinVar
Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 15, 2024 | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jun 26, 2018 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
Cadd
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Dann
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at