chr16-88707141-A-C
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 2P and 12B. PM2BP4_StrongBP6_Very_Strong
The NM_001012759.3(CTU2):c.74A>C(p.Glu25Ala) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000348 in 1,613,830 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.00074 ( 0 hom., cov: 33)
Exomes 𝑓: 0.00031 ( 1 hom. )
Consequence
CTU2
NM_001012759.3 missense
NM_001012759.3 missense
Scores
2
16
Clinical Significance
Conservation
PhyloP100: 1.46
Genes affected
CTU2 (HGNC:28005): (cytosolic thiouridylase subunit 2) This gene encodes a protein which is involved in the post-transcriptional modification of transfer RNAs (tRNAs). The encoded protein plays a role in thiolation of uridine residue present at the wobble position in a subset of tRNAs, resulting in enhanced codon reading accuracy. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Jan 2016]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -10 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
BP4
?
Computational evidence support a benign effect (MetaRNN=0.005340576).
BP6
?
Variant 16-88707141-A-C is Benign according to our data. Variant chr16-88707141-A-C is described in ClinVar as [Benign]. Clinvar id is 2906481.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CTU2 | NM_001012759.3 | c.74A>C | p.Glu25Ala | missense_variant | 2/15 | ENST00000453996.7 | |
CTU2 | NM_001318507.2 | c.74A>C | p.Glu25Ala | missense_variant | 2/15 | ||
CTU2 | NM_001012762.3 | c.74A>C | p.Glu25Ala | missense_variant | 2/14 | ||
CTU2 | NM_001318513.2 | c.-109A>C | 5_prime_UTR_variant | 2/14 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CTU2 | ENST00000453996.7 | c.74A>C | p.Glu25Ala | missense_variant | 2/15 | 1 | NM_001012759.3 | P2 |
Frequencies
GnomAD3 genomes ? AF: 0.000736 AC: 112AN: 152138Hom.: 0 Cov.: 33
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GnomAD3 exomes AF: 0.000677 AC: 170AN: 250964Hom.: 1 AF XY: 0.000736 AC XY: 100AN XY: 135832
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GnomAD4 exome AF: 0.000307 AC: 449AN: 1461574Hom.: 1 Cov.: 32 AF XY: 0.000312 AC XY: 227AN XY: 727062
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GnomAD4 genome ? AF: 0.000736 AC: 112AN: 152256Hom.: 0 Cov.: 33 AF XY: 0.00118 AC XY: 88AN XY: 74446
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ClinVar
Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
CTU2-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | May 02, 2019 | This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Dec 09, 2023 | - - |
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
Benign
Eigen_PC
Benign
FATHMM_MKL
Benign
N
LIST_S2
Benign
T;T;T
MetaRNN
Benign
T;T;T
MetaSVM
Benign
T
MutationAssessor
Benign
L;L;.
MutationTaster
Benign
N;N;N;N
PrimateAI
Uncertain
T
PROVEAN
Uncertain
N;N;N
REVEL
Benign
Sift
Benign
T;T;T
Sift4G
Benign
T;T;T
Polyphen
B;B;.
Vest4
MVP
ClinPred
T
GERP RS
RBP_binding_hub_radar
RBP_regulation_power_radar
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