chr8-116771601-A-G
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_032334.3(UTP23):c.509A>G(p.His170Arg) variant causes a missense change. The variant allele was found at a frequency of 0.00242 in 1,612,568 control chromosomes in the GnomAD database, including 98 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Genomes: 𝑓 0.013 ( 56 hom., cov: 33)
Exomes 𝑓: 0.0013 ( 42 hom. )
Consequence
UTP23
NM_032334.3 missense
NM_032334.3 missense
Scores
5
13
Clinical Significance
Conservation
PhyloP100: 5.07
Genes affected
UTP23 (HGNC:28224): (UTP23 small subunit processome component) Enables mRNA 3'-UTR binding activity and mRNA 5'-UTR binding activity. Predicted to be involved in rRNA processing. Predicted to act upstream of or within endonucleolytic cleavage in 5'-ETS of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA). Predicted to be part of small-subunit processome. Predicted to be active in nucleolus. Implicated in colorectal adenocarcinoma. [provided by Alliance of Genome Resources, Apr 2022]
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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 (MetaRNN=0.004047394).
BP6
?
Variant 8-116771601-A-G is Benign according to our data. Variant chr8-116771601-A-G is described in ClinVar as [Benign]. Clinvar id is 776379.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.0135 (2052/152312) while in subpopulation AFR AF= 0.0475 (1972/41554). AF 95% confidence interval is 0.0457. There are 56 homozygotes in gnomad4. There are 973 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd at 55 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
UTP23 | NM_032334.3 | c.509A>G | p.His170Arg | missense_variant | 3/3 | ENST00000309822.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
UTP23 | ENST00000309822.7 | c.509A>G | p.His170Arg | missense_variant | 3/3 | 1 | NM_032334.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0134 AC: 2042AN: 152194Hom.: 55 Cov.: 33
GnomAD3 genomes
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GnomAD3 exomes AF: 0.00343 AC: 855AN: 249348Hom.: 16 AF XY: 0.00234 AC XY: 315AN XY: 134680
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GnomAD4 exome AF: 0.00127 AC: 1855AN: 1460256Hom.: 42 Cov.: 31 AF XY: 0.00108 AC XY: 783AN XY: 726276
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GnomAD4 genome ? AF: 0.0135 AC: 2052AN: 152312Hom.: 56 Cov.: 33 AF XY: 0.0131 AC XY: 973AN XY: 74492
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ESP6500AA
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202
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527
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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 | Invitae | Feb 20, 2018 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
DEOGEN2
Benign
T
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Uncertain
D
LIST_S2
Benign
T
MetaRNN
Benign
T
MetaSVM
Benign
T
MutationAssessor
Uncertain
M
MutationTaster
Benign
D;D;D;D
PrimateAI
Benign
T
PROVEAN
Uncertain
D
REVEL
Benign
Sift
Benign
T
Sift4G
Benign
T
Polyphen
P
Vest4
MVP
MPC
ClinPred
T
GERP RS
Varity_R
gMVP
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