NM_001012759.3:c.36G>C
Variant names:
Variant summary
Our verdict is Likely benign. The variant received -1 ACMG points: 2P and 3B. PM2BP4_ModerateBP7
The NM_001012759.3(CTU2):c.36G>C(p.Ala12Ala) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000735 in 1,456,656 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Synonymous variant affecting the same amino acid position (i.e. A12A) has been classified as Likely benign.
Frequency
Genomes: 𝑓 0.000053 ( 0 hom., cov: 33)
Exomes 𝑓: 0.000076 ( 0 hom. )
Consequence
CTU2
NM_001012759.3 synonymous
NM_001012759.3 synonymous
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.111
Publications
1 publications found
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]
RNF166 (HGNC:28856): (ring finger protein 166) Predicted to enable ubiquitin protein ligase activity. Predicted to be involved in protein polyubiquitination and ubiquitin-dependent protein catabolic process. Predicted to be located in cytoplasm. [provided by Alliance of Genome Resources, Apr 2022]
Genome browser will be placed here
ACMG classification
Classification was made for transcript
Our verdict: Likely_benign. The variant received -1 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.46).
BP7
Synonymous conserved (PhyloP=0.111 with no splicing effect.
Variant Effect in Transcripts
ACMG analysis was done for transcript: NM_001012759.3. You can select a different transcript below to see updated ACMG assignments.
RefSeq Transcripts
| Sel. | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| CTU2 | NM_001012759.3 | MANE Select | c.36G>C | p.Ala12Ala | synonymous | Exon 1 of 15 | NP_001012777.1 | Q2VPK5-1 | |
| CTU2 | NM_001318507.2 | c.36G>C | p.Ala12Ala | synonymous | Exon 1 of 15 | NP_001305436.1 | H3BSW6 | ||
| CTU2 | NM_001012762.3 | c.36G>C | p.Ala12Ala | synonymous | Exon 1 of 14 | NP_001012780.1 | Q2VPK5-5 |
Ensembl Transcripts
| Sel. | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| CTU2 | ENST00000453996.7 | TSL:1 MANE Select | c.36G>C | p.Ala12Ala | synonymous | Exon 1 of 15 | ENSP00000388320.2 | Q2VPK5-1 | |
| CTU2 | ENST00000567949.5 | TSL:1 | c.36G>C | p.Ala12Ala | synonymous | Exon 1 of 15 | ENSP00000456908.1 | H3BSW6 | |
| CTU2 | ENST00000564105.5 | TSL:1 | n.36G>C | non_coding_transcript_exon | Exon 1 of 14 | ENSP00000454923.1 | H3BNM3 |
Frequencies
GnomAD3 genomes 0.0000526 AC: 8AN: 151986Hom.: 0 Cov.: 33 show subpopulations
GnomAD3 genomes
AF:
AC:
8
AN:
151986
Hom.:
Cov.:
33
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD4 exome AF: 0.0000759 AC: 99AN: 1304670Hom.: 0 Cov.: 31 AF XY: 0.0000606 AC XY: 39AN XY: 643530 show subpopulations
GnomAD4 exome
AF:
AC:
99
AN:
1304670
Hom.:
Cov.:
31
AF XY:
AC XY:
39
AN XY:
643530
show subpopulations
African (AFR)
AF:
AC:
0
AN:
26028
American (AMR)
AF:
AC:
0
AN:
22772
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
22730
East Asian (EAS)
AF:
AC:
0
AN:
28130
South Asian (SAS)
AF:
AC:
0
AN:
71108
European-Finnish (FIN)
AF:
AC:
0
AN:
32654
Middle Eastern (MID)
AF:
AC:
0
AN:
3884
European-Non Finnish (NFE)
AF:
AC:
97
AN:
1043406
Other (OTH)
AF:
AC:
2
AN:
53958
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.498
Heterozygous variant carriers
0
6
11
17
22
28
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Exome Het
Variant carriers
0
10
20
30
40
50
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
GnomAD4 genome 0.0000526 AC: 8AN: 151986Hom.: 0 Cov.: 33 AF XY: 0.0000404 AC XY: 3AN XY: 74238 show subpopulations
GnomAD4 genome
AF:
AC:
8
AN:
151986
Hom.:
Cov.:
33
AF XY:
AC XY:
3
AN XY:
74238
show subpopulations
African (AFR)
AF:
AC:
1
AN:
41406
American (AMR)
AF:
AC:
0
AN:
15276
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
3470
East Asian (EAS)
AF:
AC:
0
AN:
5148
South Asian (SAS)
AF:
AC:
0
AN:
4826
European-Finnish (FIN)
AF:
AC:
0
AN:
10600
Middle Eastern (MID)
AF:
AC:
0
AN:
314
European-Non Finnish (NFE)
AF:
AC:
5
AN:
67946
Other (OTH)
AF:
AC:
2
AN:
2090
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.456
Heterozygous variant carriers
0
1
2
3
4
5
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Genome Het
Variant carriers
0
2
4
6
8
10
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
Alfa
AF:
Hom.:
Bravo
AF:
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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