17-75516572-G-T

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_207346.3(TSEN54):c.12G>T(p.Glu4Asp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.682 in 1,149,816 control chromosomes in the GnomAD database, including 271,174 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★). Synonymous variant affecting the same amino acid position (i.e. E4E) has been classified as Likely benign.

Frequency

Genomes: 𝑓 0.59 ( 27373 hom., cov: 32)

Exomes 𝑓: 0.70 ( 243801 hom. )

Consequence

TSEN54
NM_207346.3 missense

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:13

Conservation

PhyloP100: -2.89

Variant links:

Genes affected

TSEN54 (HGNC:27561): (tRNA splicing endonuclease subunit 54) This gene encodes a subunit of the tRNA splicing endonuclease complex, which catalyzes the removal of introns from precursor tRNAs. The complex is also implicated in pre-mRNA 3-prime end processing. Mutations in this gene result in pontocerebellar hypoplasia type 2.[provided by RefSeq, Oct 2009]

TSEN54 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=4.9241294E-6).

BP6

Variant 17-75516572-G-T is Benign according to our data. Variant chr17-75516572-G-T is described in ClinVar as [Benign]. Clinvar id is 96673.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr17-75516572-G-T is described in Lovd as [Benign].

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.692 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TSEN54	NM_207346.3 linkuse as main transcript	c.12G>T	p.Glu4Asp	missense_variant	1/11	ENST00000333213.11

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TSEN54	ENST00000333213.11 linkuse as main transcript	c.12G>T	p.Glu4Asp	missense_variant	1/11	1	NM_207346.3	P1	Q7Z6J9-1

Frequencies

GnomAD3 genomes

AF:

0.592

AC:

88376

AN:

149396

Hom.:

27379

Cov.:

show subpopulations

Gnomad AFR

AF:

0.423

Gnomad AMI

AF:

0.828

Gnomad AMR

AF:

0.487

Gnomad ASJ

AF:

0.603

Gnomad EAS

AF:

0.520

Gnomad SAS

AF:

0.689

Gnomad FIN

AF:

0.695

Gnomad MID

AF:

0.602

Gnomad NFE

AF:

0.698

Gnomad OTH

AF:

0.596

GnomAD3 exomes

AF:

0.760

AC:

AN:

104

Hom.:

AF XY:

0.719

AC XY:

AN XY:

show subpopulations

Gnomad NFE exome

AF:

0.760

GnomAD4 exome

AF:

0.696

AC:

695858

AN:

1000312

Hom.:

243801

Cov.:

AF XY:

0.697

AC XY:

328210

AN XY:

470990

show subpopulations

Gnomad4 AFR exome

AF:

0.398

Gnomad4 AMR exome

AF:

0.454

Gnomad4 ASJ exome

AF:

0.602

Gnomad4 EAS exome

AF:

0.513

Gnomad4 SAS exome

AF:

0.710

Gnomad4 FIN exome

AF:

0.702

Gnomad4 NFE exome

AF:

0.710

Gnomad4 OTH exome

AF:

0.658

GnomAD4 genome

AF:

0.591

AC:

88389

AN:

149504

Hom.:

27373

Cov.:

AF XY:

0.590

AC XY:

43055

AN XY:

72966

show subpopulations

Gnomad4 AFR

AF:

0.423

Gnomad4 AMR

AF:

0.487

Gnomad4 ASJ

AF:

0.603

Gnomad4 EAS

AF:

0.520

Gnomad4 SAS

AF:

0.688

Gnomad4 FIN

AF:

0.695

Gnomad4 NFE

AF:

0.698

Gnomad4 OTH

AF:

0.595

Alfa

AF:

0.562

Hom.:

2148

Bravo

AF:

0.566

ExAC

AF:

0.259

AC:

181

Asia WGS

AF:

0.599

AC:

1827

AN:

3054

ClinVar

Significance: Benign

Submissions summary: Benign:13

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:6

Benign, criteria provided, single submitter	clinical testing	PreventionGenetics, part of Exact Sciences	-	- -
Benign, criteria provided, single submitter	clinical testing	Eurofins Ntd Llc (ga)	Mar 22, 2018	- -
Benign, no assertion criteria provided	clinical testing	Clinical Genetics, Academic Medical Center	-	- -
Benign, no assertion criteria provided	clinical testing	Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+	-	- -
Benign, no assertion criteria provided	clinical testing	Genome Diagnostics Laboratory, University Medical Center Utrecht	-	- -
Benign, criteria provided, single submitter	clinical testing	Genetic Services Laboratory, University of Chicago	Jul 24, 2014	- -

not provided

Benign:3

Benign, criteria provided, single submitter	clinical testing	Athena Diagnostics	Jun 14, 2017	- -
Benign, criteria provided, single submitter	clinical testing	Invitae	Feb 01, 2024	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Mar 03, 2015	- -

Pontocerebellar hypoplasia type 2A

Benign:1

Benign, criteria provided, single submitter

clinical testing

Genome-Nilou Lab

Sep 10, 2021

- -

Pontoneocerebellar hypoplasia

Benign:1

Benign, criteria provided, single submitter

clinical testing

Illumina Laboratory Services, Illumina

Jan 13, 2018

This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. -

Pontocerebellar hypoplasia type 5

Benign:1

Benign, criteria provided, single submitter

clinical testing

Genome-Nilou Lab

Sep 10, 2021

- -

Pontocerebellar hypoplasia type 4

Benign:1

Benign, criteria provided, single submitter

clinical testing

Genome-Nilou Lab

Sep 10, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.083

BayesDel_addAF

Benign

-0.71

BayesDel_noAF

Benign

-0.65

Cadd

Benign

0.043

Dann

Benign

0.80

DEOGEN2

Benign

0.0099

Eigen

Benign

-1.8

Eigen_PC

Benign

-1.9

FATHMM_MKL

Benign

0.0064

LIST_S2

Benign

0.42

MetaRNN

Benign

0.0000049

MetaSVM

Benign

-1.0

MutationAssessor

Benign

1.4

MutationTaster

Benign

1.0

PrimateAI

Pathogenic

0.86

PROVEAN

Benign

-0.18

REVEL

Benign

0.059

Sift

Benign

0.30

Sift4G

Benign

0.13

Polyphen

0.0

Vest4

0.022

MutPred

0.15

Loss of glycosylation at P3 (P = 0.0618);

MPC

0.23

ClinPred

0.087

GERP RS

-8.9

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.0

Varity_R

0.037

gMVP

0.14

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

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