Variant 1-100144083-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_ModerateBP7BA1

The NM_019083.3(TRMT13):c.757C>T(p.Leu253Leu) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0449 in 1,611,528 control chromosomes in the GnomAD database, including 1,830 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.049 ( 209 hom., cov: 32)

Exomes 𝑓: 0.045 ( 1621 hom. )

Consequence

TRMT13
NM_019083.3 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 2.01

Variant links:

Genes affected

TRMT13 (HGNC:25502): (tRNA methyltransferase 13 homolog) Predicted to enable tRNA methyltransferase activity. Predicted to be involved in tRNA methylation. [provided by Alliance of Genome Resources, Apr 2022]

TRMT13 links:

TRMT13 (HGNC:):

TRMT13 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -11 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.39).

BP7

Synonymous conserved (PhyloP=2.01 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0652 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TRMT13	NM_019083.3 linkuse as main transcript	c.757C>T	p.Leu253Leu	synonymous_variant	9/11	ENST00000370141.8	NP_061956.2	Q9NUP7-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	UniProt
TRMT13	ENST00000370141.8 linkuse as main transcript	c.757C>T	p.Leu253Leu	synonymous_variant	9/11	1	NM_019083.3	ENSP00000359160.2	Q9NUP7-1
TRMT13	ENST00000482437.5 linkuse as main transcript	n.*566C>T		non_coding_transcript_exon_variant	8/8	2		ENSP00000432616.1	Q9NUP7-2
TRMT13	ENST00000493651.1 linkuse as main transcript	n.318C>T		non_coding_transcript_exon_variant	2/2	2
TRMT13	ENST00000482437.5 linkuse as main transcript	n.*566C>T		3_prime_UTR_variant	8/8	2		ENSP00000432616.1	Q9NUP7-2

Frequencies

GnomAD3 genomes

AF:

0.0487

AC:

7402

AN:

152024

Hom.:

210

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0673

Gnomad AMI

AF:

0.0482

Gnomad AMR

AF:

0.0330

Gnomad ASJ

AF:

0.0133

Gnomad EAS

AF:

0.0156

Gnomad SAS

AF:

0.0545

Gnomad FIN

AF:

0.0407

Gnomad MID

AF:

0.0285

Gnomad NFE

AF:

0.0462

Gnomad OTH

AF:

0.0475

GnomAD3 exomes

AF:

0.0379

AC:

9510

AN:

250970

Hom.:

226

AF XY:

0.0389

AC XY:

5280

AN XY:

135660

show subpopulations

Gnomad AFR exome

AF:

0.0674

Gnomad AMR exome

AF:

0.0174

Gnomad ASJ exome

AF:

0.0153

Gnomad EAS exome

AF:

0.00468

Gnomad SAS exome

AF:

0.0542

Gnomad FIN exome

AF:

0.0392

Gnomad NFE exome

AF:

0.0427

Gnomad OTH exome

AF:

0.0371

GnomAD4 exome

AF:

0.0445

AC:

64995

AN:

1459386

Hom.:

1621

Cov.:

AF XY:

0.0448

AC XY:

32513

AN XY:

726180

show subpopulations

Gnomad4 AFR exome

AF:

0.0704

Gnomad4 AMR exome

AF:

0.0194

Gnomad4 ASJ exome

AF:

0.0154

Gnomad4 EAS exome

AF:

0.0319

Gnomad4 SAS exome

AF:

0.0548

Gnomad4 FIN exome

AF:

0.0390

Gnomad4 NFE exome

AF:

0.0455

Gnomad4 OTH exome

AF:

0.0413

GnomAD4 genome

AF:

0.0487

AC:

7404

AN:

152142

Hom.:

209

Cov.:

AF XY:

0.0487

AC XY:

3624

AN XY:

74368

show subpopulations

Gnomad4 AFR

AF:

0.0673

Gnomad4 AMR

AF:

0.0330

Gnomad4 ASJ

AF:

0.0133

Gnomad4 EAS

AF:

0.0157

Gnomad4 SAS

AF:

0.0541

Gnomad4 FIN

AF:

0.0407

Gnomad4 NFE

AF:

0.0462

Gnomad4 OTH

AF:

0.0460

Alfa

AF:

0.0428

Hom.:

251

Bravo

AF:

0.0465

Asia WGS

AF:

0.0320

AC:

111

AN:

3476

EpiCase

AF:

0.0412

EpiControl

AF:

0.0387

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.39

CADD

Benign

DANN

Benign

0.66

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over