chr10-120851418-G-A
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_018117.12(WDR11):c.-3G>A variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0015 in 1,609,232 control chromosomes in the GnomAD database, including 30 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.0067 ( 17 hom., cov: 33)
Exomes 𝑓: 0.00095 ( 13 hom. )
Consequence
WDR11
NM_018117.12 5_prime_UTR
NM_018117.12 5_prime_UTR
Scores
2
Clinical Significance
Conservation
PhyloP100: 1.54
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=-0.53).
BP6
?
Variant 10-120851418-G-A is Benign according to our data. Variant chr10-120851418-G-A is described in ClinVar as [Benign]. Clinvar id is 1177878.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.0067 (1020/152348) while in subpopulation AFR AF= 0.0224 (933/41572). AF 95% confidence interval is 0.0212. There are 17 homozygotes in gnomad4. There are 473 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.
BS2
?
High AC in GnomAd at 1017 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
WDR11 | NM_018117.12 | c.-3G>A | 5_prime_UTR_variant | 1/29 | ENST00000263461.11 | ||
WDR11 | XM_005269963.3 | c.-801G>A | 5_prime_UTR_variant | 1/29 | |||
WDR11 | XR_007061973.1 | n.57G>A | non_coding_transcript_exon_variant | 1/20 | |||
WDR11 | XR_428707.4 | n.57G>A | non_coding_transcript_exon_variant | 1/28 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
WDR11 | ENST00000263461.11 | c.-3G>A | 5_prime_UTR_variant | 1/29 | 1 | NM_018117.12 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00668 AC: 1017AN: 152230Hom.: 17 Cov.: 33
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GnomAD3 exomes AF: 0.00181 AC: 430AN: 238084Hom.: 7 AF XY: 0.00142 AC XY: 184AN XY: 129542
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GnomAD4 exome AF: 0.000954 AC: 1390AN: 1456884Hom.: 13 Cov.: 31 AF XY: 0.000840 AC XY: 608AN XY: 724218
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GnomAD4 genome ? AF: 0.00670 AC: 1020AN: 152348Hom.: 17 Cov.: 33 AF XY: 0.00635 AC XY: 473AN XY: 74506
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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 | Oct 12, 2020 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
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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