16-88707117-C-T
Position:
Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP4_StrongBP6_Very_StrongBS2
The NM_001012759.3(CTU2):c.69-19C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00482 in 1,612,104 control chromosomes in the GnomAD database, including 22 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Genomes: 𝑓 0.0037 ( 3 hom., cov: 33)
Exomes 𝑓: 0.0049 ( 19 hom. )
Consequence
CTU2
NM_001012759.3 intron
NM_001012759.3 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.715
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 Benign. Variant got -16 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.88).
BP6
Variant 16-88707117-C-T is Benign according to our data. Variant chr16-88707117-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 1600007.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BS2
High Homozygotes in GnomAd4 at 3 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CTU2 | NM_001012759.3 | c.69-19C>T | intron_variant | ENST00000453996.7 | |||
CTU2 | NM_001012762.3 | c.69-19C>T | intron_variant | ||||
CTU2 | NM_001318507.2 | c.69-19C>T | intron_variant | ||||
CTU2 | NM_001318513.2 | c.-114-19C>T | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CTU2 | ENST00000453996.7 | c.69-19C>T | intron_variant | 1 | NM_001012759.3 | P2 |
Frequencies
GnomAD3 genomes AF: 0.00365 AC: 556AN: 152142Hom.: 3 Cov.: 33
GnomAD3 genomes
AF:
AC:
556
AN:
152142
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:
GnomAD3 exomes AF: 0.00371 AC: 929AN: 250740Hom.: 7 AF XY: 0.00356 AC XY: 484AN XY: 135782
GnomAD3 exomes
AF:
AC:
929
AN:
250740
Hom.:
AF XY:
AC XY:
484
AN XY:
135782
Gnomad AFR exome
AF:
Gnomad AMR exome
AF:
Gnomad ASJ exome
AF:
Gnomad EAS exome
AF:
Gnomad SAS exome
AF:
Gnomad FIN exome
AF:
Gnomad NFE exome
AF:
Gnomad OTH exome
AF:
GnomAD4 exome AF: 0.00494 AC: 7217AN: 1459844Hom.: 19 Cov.: 30 AF XY: 0.00485 AC XY: 3521AN XY: 726036
GnomAD4 exome
AF:
AC:
7217
AN:
1459844
Hom.:
Cov.:
30
AF XY:
AC XY:
3521
AN XY:
726036
Gnomad4 AFR exome
AF:
Gnomad4 AMR exome
AF:
Gnomad4 ASJ exome
AF:
Gnomad4 EAS exome
AF:
Gnomad4 SAS exome
AF:
Gnomad4 FIN exome
AF:
Gnomad4 NFE exome
AF:
Gnomad4 OTH exome
AF:
GnomAD4 genome AF: 0.00365 AC: 556AN: 152260Hom.: 3 Cov.: 33 AF XY: 0.00320 AC XY: 238AN XY: 74430
GnomAD4 genome
AF:
AC:
556
AN:
152260
Hom.:
Cov.:
33
AF XY:
AC XY:
238
AN XY:
74430
Gnomad4 AFR
AF:
Gnomad4 AMR
AF:
Gnomad4 ASJ
AF:
Gnomad4 EAS
AF:
Gnomad4 SAS
AF:
Gnomad4 FIN
AF:
Gnomad4 NFE
AF:
Gnomad4 OTH
AF:
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
4
AN:
3478
ClinVar
Significance: Benign/Likely benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 08, 2024 | - - |
Microcephaly, facial dysmorphism, renal agenesis, and ambiguous genitalia syndrome Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Fulgent Genetics, Fulgent Genetics | Nov 18, 2021 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
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