chr16-88714227-G-GGTGTGTGTGGGTGTGTGTGGGTGT
Variant summary
Our verdict is Likely benign. Variant got -1 ACMG points: 0P and 1B. BP3
The NM_001012759.3(CTU2):c.1097+5_1097+6insTGTGGGTGTGTGTGGGTGTGTGTG variant causes a inframe insertion, splice region change. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.000024 ( 0 hom., cov: 0)
Consequence
CTU2
NM_001012759.3 inframe_insertion, splice_region
NM_001012759.3 inframe_insertion, splice_region
Scores
Not classified
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 5.54
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 -1 ACMG points.
BP3
?
Nonframeshift variant in repetitive region in NM_001012759.3
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CTU2 | NM_001012759.3 | c.1097+5_1097+6insTGTGGGTGTGTGTGGGTGTGTGTG | inframe_insertion, splice_region_variant | ENST00000453996.7 | |||
CTU2 | NM_001012762.3 | c.1097+5_1097+6insTGTGGGTGTGTGTGGGTGTGTGTG | inframe_insertion, splice_region_variant | ||||
CTU2 | NM_001318507.2 | c.1310+5_1310+6insTGTGGGTGTGTGTGGGTGTGTGTG | inframe_insertion, splice_region_variant | ||||
CTU2 | NM_001318513.2 | c.836+5_836+6insTGTGGGTGTGTGTGGGTGTGTGTG | inframe_insertion, splice_region_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CTU2 | ENST00000453996.7 | c.1097+5_1097+6insTGTGGGTGTGTGTGGGTGTGTGTG | inframe_insertion, splice_region_variant | 1 | NM_001012759.3 | P2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000237 AC: 1AN: 42254Hom.: 0 Cov.: 0
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GnomAD4 genome ? AF: 0.0000237 AC: 1AN: 42254Hom.: 0 Cov.: 0 AF XY: 0.0000499 AC XY: 1AN XY: 20030
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ClinVar
Not reported inComputational scores
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Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at