chr5-111111042-C-A
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Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_139281.3(WDR36):c.1607+89C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.467 in 1,557,842 control chromosomes in the GnomAD database, including 175,411 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.51 ( 20145 hom., cov: 32)
Exomes 𝑓: 0.46 ( 155266 hom. )
Consequence
WDR36
NM_139281.3 intron
NM_139281.3 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -1.95
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 -14 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.91).
BP6
Variant 5-111111042-C-A is Benign according to our data. Variant chr5-111111042-C-A is described in ClinVar as [Benign]. Clinvar id is 1263868.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.653 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
WDR36 | NM_139281.3 | c.1607+89C>A | intron_variant | ENST00000513710.4 | |||
WDR36 | XM_047416729.1 | c.1607+89C>A | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
WDR36 | ENST00000513710.4 | c.1607+89C>A | intron_variant | 1 | NM_139281.3 | P1 | |||
WDR36 | ENST00000505303.5 | n.1743+89C>A | intron_variant, non_coding_transcript_variant | 5 |
Frequencies
GnomAD3 genomes AF: 0.509 AC: 76975AN: 151214Hom.: 20119 Cov.: 32
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GnomAD4 exome AF: 0.463 AC: 650627AN: 1406510Hom.: 155266 Cov.: 24 AF XY: 0.469 AC XY: 329436AN XY: 703026
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GnomAD4 genome AF: 0.509 AC: 77054AN: 151332Hom.: 20145 Cov.: 32 AF XY: 0.516 AC XY: 38117AN XY: 73916
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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
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jun 26, 2018 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at