chr16-88707228-C-A
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Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_001012759.3(CTU2):c.143+18C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000447 in 1,612,162 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.0000066 ( 0 hom., cov: 33)
Exomes 𝑓: 0.000049 ( 1 hom. )
Consequence
CTU2
NM_001012759.3 intron
NM_001012759.3 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -6.45
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 Likely_benign. Variant got -4 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.89).
BP6
Variant 16-88707228-C-A is Benign according to our data. Variant chr16-88707228-C-A is described in ClinVar as [Likely_benign]. Clinvar id is 1921261.Status of the report is criteria_provided_single_submitter, 1 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CTU2 | NM_001012759.3 | c.143+18C>A | intron_variant | ENST00000453996.7 | |||
CTU2 | NM_001012762.3 | c.143+18C>A | intron_variant | ||||
CTU2 | NM_001318507.2 | c.143+18C>A | intron_variant | ||||
CTU2 | NM_001318513.2 | c.-40+18C>A | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CTU2 | ENST00000453996.7 | c.143+18C>A | intron_variant | 1 | NM_001012759.3 | P2 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152268Hom.: 0 Cov.: 33
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GnomAD3 exomes AF: 0.0000958 AC: 24AN: 250612Hom.: 0 AF XY: 0.000111 AC XY: 15AN XY: 135746
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GnomAD4 exome AF: 0.0000486 AC: 71AN: 1459776Hom.: 1 Cov.: 31 AF XY: 0.0000606 AC XY: 44AN XY: 725976
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GnomAD4 genome AF: 0.00000656 AC: 1AN: 152386Hom.: 0 Cov.: 33 AF XY: 0.0000134 AC XY: 1AN XY: 74518
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Sep 06, 2022 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at