Variant chr1-39883459-G-A 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_017646.6(TRIT1):c.33C>T(p.Pro11=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.421 in 1,603,634 control chromosomes in the GnomAD database, including 144,664 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.46 ( 16390 hom., cov: 32)

Exomes 𝑓: 0.42 ( 128274 hom. )

Consequence

TRIT1
NM_017646.6 synonymous

Scores

Clinical Significance

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

Conservation

PhyloP100: -0.156

Variant links:

Genes affected

TRIT1 (HGNC:20286): (tRNA isopentenyltransferase 1) This gene encodes a protein that that is targeted to the mitochondrion and modifies transfer RNAs (tRNAs) by adding a dimethylallyl group onto the adenine at position 37. This modification is important for maintaining the correct reading frame during protein translation. This gene is considered a tumor suppressor and its expression can decrease cell growth. Alternative splicing results in multiple transcripts variants, most of which are likely non-functional. [provided by RefSeq, Aug 2015]

TRIT1 links:

MYCL-AS1 (HGNC:):

MYCL-AS1 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=-0.67).

BP6

Variant 1-39883459-G-A is Benign according to our data. Variant chr1-39883459-G-A is described in ClinVar as [Benign]. Clinvar id is 1342274.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=-0.156 with no splicing effect.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.578 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TRIT1	NM_017646.6 linkuse as main transcript	c.33C>T	p.Pro11=	synonymous_variant	1/11	ENST00000316891.10
MYCL-AS1	NR_183424.1 linkuse as main transcript	n.272+38G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TRIT1	ENST00000316891.10 linkuse as main transcript	c.33C>T	p.Pro11=	synonymous_variant	1/11	1	NM_017646.6	P1	Q9H3H1-1

Frequencies

GnomAD3 genomes

AF:

0.457

AC:

69412

AN:

151940

Hom.:

16359

Cov.:

show subpopulations

Gnomad AFR

AF:

0.576

Gnomad AMI

AF:

0.209

Gnomad AMR

AF:

0.432

Gnomad ASJ

AF:

0.474

Gnomad EAS

AF:

0.596

Gnomad SAS

AF:

0.456

Gnomad FIN

AF:

0.398

Gnomad MID

AF:

0.285

Gnomad NFE

AF:

0.393

Gnomad OTH

AF:

0.414

GnomAD3 exomes

AF:

0.442

AC:

108640

AN:

246060

Hom.:

24629

AF XY:

0.434

AC XY:

58089

AN XY:

133950

show subpopulations

Gnomad AFR exome

AF:

0.582

Gnomad AMR exome

AF:

0.472

Gnomad ASJ exome

AF:

0.466

Gnomad EAS exome

AF:

0.595

Gnomad SAS exome

AF:

0.448

Gnomad FIN exome

AF:

0.403

Gnomad NFE exome

AF:

0.392

Gnomad OTH exome

AF:

0.411

GnomAD4 exome

AF:

0.418

AC:

606042

AN:

1451576

Hom.:

128274

Cov.:

AF XY:

0.417

AC XY:

300368

AN XY:

719920

show subpopulations

Gnomad4 AFR exome

AF:

0.583

Gnomad4 AMR exome

AF:

0.461

Gnomad4 ASJ exome

AF:

0.474

Gnomad4 EAS exome

AF:

0.603

Gnomad4 SAS exome

AF:

0.444

Gnomad4 FIN exome

AF:

0.408

Gnomad4 NFE exome

AF:

0.401

Gnomad4 OTH exome

AF:

0.432

GnomAD4 genome

AF:

0.457

AC:

69491

AN:

152058

Hom.:

16390

Cov.:

AF XY:

0.456

AC XY:

33903

AN XY:

74334

show subpopulations

Gnomad4 AFR

AF:

0.576

Gnomad4 AMR

AF:

0.433

Gnomad4 ASJ

AF:

0.474

Gnomad4 EAS

AF:

0.596

Gnomad4 SAS

AF:

0.455

Gnomad4 FIN

AF:

0.398

Gnomad4 NFE

AF:

0.393

Gnomad4 OTH

AF:

0.414

Alfa

AF:

0.424

Hom.:

10113

Bravo

AF:

0.465

Asia WGS

AF:

0.555

AC:

1930

AN:

3478

EpiCase

AF:

0.390

EpiControl

AF:

0.384

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	Labcorp Genetics (formerly Invitae), Labcorp	Feb 01, 2024	- -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

Combined oxidative phosphorylation deficiency 35

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

BayesDel_noAF

Benign

-0.67

CADD

Benign

7.6

DANN

Benign

0.83

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.7

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