16-88706598-G-C

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong

The NM_001012759.3(CTU2):ā€‹c.68G>Cā€‹(p.Ser23Thr) variant causes a missense, splice region change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000523 in 1,432,692 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/22 in silico tools predict a benign outcome for this variant. 2/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Uncertain significance (ā˜…).

Frequency

Genomes: š‘“ 0.00011 ( 0 hom., cov: 33)
Exomes š‘“: 0.000045 ( 0 hom. )

Consequence

CTU2
NM_001012759.3 missense, splice_region

Scores

1
18
Splicing: ADA: 0.9948
1
1

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 1.04
Variant links:
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.05778572).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
CTU2NM_001012759.3 linkuse as main transcriptc.68G>C p.Ser23Thr missense_variant, splice_region_variant 1/15 ENST00000453996.7
CTU2NM_001318507.2 linkuse as main transcriptc.68G>C p.Ser23Thr missense_variant, splice_region_variant 1/15
CTU2NM_001012762.3 linkuse as main transcriptc.68G>C p.Ser23Thr missense_variant, splice_region_variant 1/14
CTU2NM_001318513.2 linkuse as main transcriptc.-115G>C splice_region_variant, 5_prime_UTR_variant 1/14

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
CTU2ENST00000453996.7 linkuse as main transcriptc.68G>C p.Ser23Thr missense_variant, splice_region_variant 1/151 NM_001012759.3 P2Q2VPK5-1

Frequencies

GnomAD3 genomes
AF:
0.000118
AC:
18
AN:
152048
Hom.:
0
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.00
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.000523
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.000147
Gnomad OTH
AF:
0.00
GnomAD3 exomes
AF:
0.000125
AC:
6
AN:
47850
Hom.:
0
AF XY:
0.000103
AC XY:
3
AN XY:
29042
show subpopulations
Gnomad AFR exome
AF:
0.00
Gnomad AMR exome
AF:
0.000696
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.00
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.0000545
Gnomad OTH exome
AF:
0.00
GnomAD4 exome
AF:
0.0000453
AC:
58
AN:
1280534
Hom.:
0
Cov.:
31
AF XY:
0.0000492
AC XY:
31
AN XY:
630358
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.000631
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.0000435
Gnomad4 OTH exome
AF:
0.0000379
GnomAD4 genome
AF:
0.000112
AC:
17
AN:
152158
Hom.:
0
Cov.:
33
AF XY:
0.0000941
AC XY:
7
AN XY:
74402
show subpopulations
Gnomad4 AFR
AF:
0.00
Gnomad4 AMR
AF:
0.000457
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.000147
Gnomad4 OTH
AF:
0.00
Bravo
AF:
0.0000869

ClinVar

Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not provided Uncertain:1
Uncertain significance, criteria provided, single submitterclinical testingGeneDxDec 15, 2023In silico analysis supports that this missense variant does not alter protein structure/function; Has not been previously published as pathogenic or benign to our knowledge -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.087
BayesDel_addAF
Benign
-0.53
T
BayesDel_noAF
Benign
-0.62
CADD
Uncertain
24
DANN
Benign
0.80
DEOGEN2
Benign
0.0023
T;.;.
Eigen
Benign
-0.62
Eigen_PC
Benign
-0.62
FATHMM_MKL
Benign
0.0012
N
LIST_S2
Benign
0.41
T;T;T
M_CAP
Benign
0.068
D
MetaRNN
Benign
0.058
T;T;T
MetaSVM
Benign
-1.0
T
MutationAssessor
Benign
1.8
L;L;.
MutationTaster
Benign
1.0
D;N;N;N
PrimateAI
Uncertain
0.72
T
PROVEAN
Benign
-1.0
N;N;N
REVEL
Benign
0.078
Sift
Benign
0.34
T;T;T
Sift4G
Benign
0.53
T;T;T
Polyphen
0.0020
B;B;.
Vest4
0.095
MutPred
0.18
Gain of glycosylation at S23 (P = 0.0382);Gain of glycosylation at S23 (P = 0.0382);Gain of glycosylation at S23 (P = 0.0382);
MVP
0.17
ClinPred
0.025
T
GERP RS
3.2
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
2.7
Varity_R
0.13
gMVP
0.38

Splicing

Name
Calibrated prediction
Score
Prediction
dbscSNV1_ADA
Pathogenic
0.99
dbscSNV1_RF
Benign
0.67
SpliceAI score (max)
0.070
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs536176202; hg19: chr16-88773006; API