chr10-120851649-T-C
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_018117.12(WDR11):c.86+143T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00175 in 973,742 control chromosomes in the GnomAD database, including 18 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.0070 ( 8 hom., cov: 33)
Exomes 𝑓: 0.00079 ( 10 hom. )
Consequence
WDR11
NM_018117.12 intron
NM_018117.12 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -2.10
Genes affected
WDR11 (HGNC:13831): (WD repeat domain 11) 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. This gene is located in the chromosome 10q25-26 region, which is frequently deleted in gliomas and tumors of other tissues, and is disrupted by the t(10;19) translocation rearrangement in glioblastoma cells. The gene location suggests that it is a candidate gene for the tumor suppressor locus. [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=-0.8).
BP6
?
Variant 10-120851649-T-C is Benign according to our data. Variant chr10-120851649-T-C is described in ClinVar as [Likely_benign]. Clinvar id is 1196688.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00695 (1059/152332) while in subpopulation AFR AF= 0.0238 (990/41574). AF 95% confidence interval is 0.0226. There are 8 homozygotes in gnomad4. There are 500 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.
BS2
?
High AC in GnomAd at 1059 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
WDR11 | NM_018117.12 | c.86+143T>C | intron_variant | ENST00000263461.11 | |||
WDR11 | XM_005269963.3 | c.-692+122T>C | intron_variant | ||||
WDR11 | XR_007061973.1 | n.145+143T>C | intron_variant, non_coding_transcript_variant | ||||
WDR11 | XR_428707.4 | n.145+143T>C | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
WDR11 | ENST00000263461.11 | c.86+143T>C | intron_variant | 1 | NM_018117.12 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00696 AC: 1059AN: 152214Hom.: 8 Cov.: 33
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GnomAD4 exome AF: 0.000786 AC: 646AN: 821410Hom.: 10 Cov.: 11 AF XY: 0.000637 AC XY: 268AN XY: 421028
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | May 20, 2019 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
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Dann
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at