16-88714227-GGTGT-GGTGTGTGTGGGTGTGTGTGGGTGTGTGT

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
• 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]

ACMG classification

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: 1 AN: 42254 Hom.: 0 Cov.: 0

Gnomad AFR AF: 0.00

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.000321

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00

Gnomad OTH AF: 0.00

GnomAD4 exome Cov.: 0

GnomAD4 genome AF: 0.0000237 AC: 1 AN: 42254 Hom.: 0 Cov.: 0 AF XY: 0.0000499 AC XY: 1 AN XY: 20030

Gnomad4 AFR AF: 0.00

Gnomad4 AMR AF: 0.00

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.000321

Gnomad4 NFE AF: 0.00

Gnomad4 OTH AF: 0.00

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs149847195; hg19: chr16-88780635;