Variant 16-88714227-GGTGT-GGTGTGTGT details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP6_Very_Strong

The NM_001012759.3(CTU2):c.1097+2_1097+5dupTGTG variant causes a splice region, intron change. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.46 ( 1367 hom., cov: 0)

Exomes 𝑓: 0.51 ( 14071 hom. )

Failed GnomAD Quality Control

Consequence

CTU2
NM_001012759.3 splice_region, intron

Scores

Not classified

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:3

Conservation

PhyloP100: 5.54

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]

CTU2 links:

CTU2 (HGNC:):

CTU2 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -8 ACMG points.

BP6

Variant 16-88714227-G-GGTGT is Benign according to our data. Variant chr16-88714227-G-GGTGT is described in ClinVar as [Benign]. Clinvar id is 402575.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	MANE	Protein	UniProt
CTU2	NM_001012759.3 linkuse as main transcript	c.1097+2_1097+5dupTGTG	splice_region_variant, intron_variant	ENST00000453996.7	NP_001012777.1	Q2VPK5-1
CTU2	NM_001318507.2 linkuse as main transcript	c.1310+2_1310+5dupTGTG	splice_region_variant, intron_variant		NP_001305436.1	Q2VPK5H3BSW6
CTU2	NM_001012762.3 linkuse as main transcript	c.1097+2_1097+5dupTGTG	splice_region_variant, intron_variant		NP_001012780.1	Q2VPK5-5
CTU2	NM_001318513.2 linkuse as main transcript	c.836+2_836+5dupTGTG	splice_region_variant, intron_variant		NP_001305442.1	Q2VPK5-3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CTU2	ENST00000453996.7 linkuse as main transcript	c.1097+2_1097+5dupTGTG		splice_region_variant, intron_variant		1	NM_001012759.3	ENSP00000388320.2		Q2VPK5-1

Frequencies

GnomAD3 genomes

AF:

0.00

AC:

19378

AN:

42188

Hom.:

1368

Cov.:

FAILED QC

Gnomad AFR

AF:

0.405

Gnomad AMI

AF:

0.514

Gnomad AMR

AF:

0.373

Gnomad ASJ

AF:

0.437

Gnomad EAS

AF:

0.0385

Gnomad SAS

AF:

0.333

Gnomad FIN

AF:

0.495

Gnomad MID

AF:

0.400

Gnomad NFE

AF:

0.517

Gnomad OTH

AF:

0.457

GnomAD3 exomes

AF:

0.104

AC:

25883

AN:

248558

Hom.:

1889

AF XY:

0.102

AC XY:

13743

AN XY:

134954

show subpopulations

Gnomad AFR exome

AF:

0.166

Gnomad AMR exome

AF:

0.0416

Gnomad ASJ exome

AF:

0.0905

Gnomad EAS exome

AF:

0.000109

Gnomad SAS exome

AF:

0.0297

Gnomad FIN exome

AF:

0.148

Gnomad NFE exome

AF:

0.145

Gnomad OTH exome

AF:

0.110

GnomAD4 exome

Data not reliable, filtered out with message: InbreedingCoeff

AF:

0.507

AC:

190517

AN:

375902

Hom.:

14071

Cov.:

AF XY:

0.507

AC XY:

92586

AN XY:

182542

show subpopulations

Gnomad4 AFR exome

AF:

0.397

Gnomad4 AMR exome

AF:

0.386

Gnomad4 ASJ exome

AF:

0.445

Gnomad4 EAS exome

AF:

0.0307

Gnomad4 SAS exome

AF:

0.377

Gnomad4 FIN exome

AF:

0.513

Gnomad4 NFE exome

AF:

0.519

Gnomad4 OTH exome

AF:

0.482

GnomAD4 genome

Data not reliable, filtered out with message: InbreedingCoeff

AF:

0.459

AC:

19380

AN:

42226

Hom.:

1367

Cov.:

AF XY:

0.455

AC XY:

9121

AN XY:

20030

show subpopulations

Gnomad4 AFR

AF:

0.404

Gnomad4 AMR

AF:

0.373

Gnomad4 ASJ

AF:

0.437

Gnomad4 EAS

AF:

0.0385

Gnomad4 SAS

AF:

0.333

Gnomad4 FIN

AF:

0.495

Gnomad4 NFE

AF:

0.517

Gnomad4 OTH

AF:

0.452

EpiCase

AF:

0.128

EpiControl

AF:

0.119

ClinVar

Significance: Benign

Submissions summary: Benign:3

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	clinical testing	GeneDx	Apr 27, 2021	- -
Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Jan 24, 2024	- -

not specified

Benign:1

Benign, criteria provided, single submitter

clinical testing

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Mar 28, 2016

Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: Frequency (fails inbreeding coefficient filter) -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over