Variant 3-3140611-G-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1

The NM_182916.3(TRNT1):c.444G>T(p.Ala148Ala) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0178 in 1,613,944 control chromosomes in the GnomAD database, including 609 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.040 ( 242 hom., cov: 34)

Exomes 𝑓: 0.016 ( 367 hom. )

Consequence

TRNT1
NM_182916.3 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:5

Conservation

PhyloP100: -0.578

Variant links:

Genes affected

TRNT1 (HGNC:17341): (tRNA nucleotidyl transferase 1) The protein encoded by this gene is a CCA-adding enzyme which belongs to the tRNA nucleotidyltransferase/poly(A) polymerase family. This essential enzyme functions by catalyzing the addition of the conserved nucleotide triplet CCA to the 3' terminus of tRNA molecules. Mutations in this gene result in sideroblastic anemia with B-cell immunodeficiency, periodic fevers, and developmental delay. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Dec 2014]

TRNT1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.68).

BP6

Variant 3-3140611-G-T is Benign according to our data. Variant chr3-3140611-G-T is described in ClinVar as [Benign]. Clinvar id is 380599.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=-0.578 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.106 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TRNT1	NM_182916.3 link	c.444G>T	p.Ala148Ala	synonymous_variant	4/8	ENST00000251607.11	NP_886552.3	Q96Q11-1A0A024R2H7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TRNT1	ENST00000251607.11 link	c.444G>T	p.Ala148Ala	synonymous_variant	4/8	1	NM_182916.3	ENSP00000251607.6		Q96Q11-1

Frequencies

GnomAD3 genomes

AF:

0.0393

AC:

5986

AN:

152134

Hom.:

239

Cov.:

show subpopulations

Gnomad AFR

AF:

0.108

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0291

Gnomad ASJ

AF:

0.00749

Gnomad EAS

AF:

0.00366

Gnomad SAS

AF:

0.00497

Gnomad FIN

AF:

0.000849

Gnomad MID

AF:

0.0222

Gnomad NFE

AF:

0.0133

Gnomad OTH

AF:

0.0411

GnomAD3 exomes

AF:

0.0162

AC:

4063

AN:

251422

Hom.:

102

AF XY:

0.0140

AC XY:

1905

AN XY:

135892

show subpopulations

Gnomad AFR exome

AF:

0.115

Gnomad AMR exome

AF:

0.0128

Gnomad ASJ exome

AF:

0.00933

Gnomad EAS exome

AF:

0.00288

Gnomad SAS exome

AF:

0.00317

Gnomad FIN exome

AF:

0.00125

Gnomad NFE exome

AF:

0.0123

Gnomad OTH exome

AF:

0.0132

GnomAD4 exome

AF:

0.0155

AC:

22698

AN:

1461692

Hom.:

367

Cov.:

AF XY:

0.0150

AC XY:

10884

AN XY:

727156

show subpopulations

Gnomad4 AFR exome

AF:

0.109

Gnomad4 AMR exome

AF:

0.0142

Gnomad4 ASJ exome

AF:

0.00953

Gnomad4 EAS exome

AF:

0.00154

Gnomad4 SAS exome

AF:

0.00347

Gnomad4 FIN exome

AF:

0.00210

Gnomad4 NFE exome

AF:

0.0148

Gnomad4 OTH exome

AF:

0.0192

GnomAD4 genome

AF:

0.0395

AC:

6015

AN:

152252

Hom.:

242

Cov.:

AF XY:

0.0372

AC XY:

2769

AN XY:

74434

show subpopulations

Gnomad4 AFR

AF:

0.108

Gnomad4 AMR

AF:

0.0290

Gnomad4 ASJ

AF:

0.00749

Gnomad4 EAS

AF:

0.00367

Gnomad4 SAS

AF:

0.00518

Gnomad4 FIN

AF:

0.000849

Gnomad4 NFE

AF:

0.0133

Gnomad4 OTH

AF:

0.0412

Alfa

AF:

0.0215

Hom.:

Bravo

AF:

0.0448

Asia WGS

AF:

0.0220

AC:

AN:

3478

EpiCase

AF:

0.0136

EpiControl

AF:

0.0136

ClinVar

Significance: Benign

Submissions summary: Benign:5

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:2

Benign, criteria provided, single submitter	clinical testing	Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine	Mar 29, 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 -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Dec 22, 2015	This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -

not provided

Benign:1

Benign, criteria provided, single submitter

not provided

Breakthrough Genomics, Breakthrough Genomics

- -

Retinal dystrophy

Benign:1

Benign, criteria provided, single submitter

research

Dept Of Ophthalmology, Nagoya University

Oct 01, 2023

- -

Congenital sideroblastic anemia-B-cell immunodeficiency-periodic fever-developmental delay syndrome

Benign:1

Benign, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Feb 03, 2025

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.68

CADD

Benign

6.0

DANN

Benign

0.62

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.7

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.14

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