rs687513

chr1-100133311-C-Achr1-100133311-C-T

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The NM_019083.3(TRMT13):c.143C>A(p.Ala48Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 12/20 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. A48T) has been classified as Benign.

• Frequency: Genomes: not found (cov: 30)
• Consequence: TRMT13 NM_019083.3 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.50

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]

ACMG classification

Verdict is Uncertain_significance. Variant got 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.15127453).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TRMT13	NM_019083.3	c.143C>A	p.Ala48Glu	missense_variant	1/11	ENST00000370141.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TRMT13	ENST00000370141.8	c.143C>A	p.Ala48Glu	missense_variant	1/11	1	NM_019083.3	P1
TRMT13	ENST00000370139.1	c.50C>A	p.Ala17Glu	missense_variant	1/6	3
TRMT13	ENST00000370143.5	c.143C>A	p.Ala48Glu	missense_variant	1/5	3
TRMT13	ENST00000482437.5	c.143C>A	p.Ala48Glu	missense_variant, NMD_transcript_variant	1/8	2

Frequencies

GnomAD3 genomes Cov.: 30

GnomAD4 exome Cov.: 54

GnomAD4 genome Cov.: 30

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.17
BayesDel_addAF	Benign	-0.11	T
BayesDel_noAF	Benign	-0.40
Cadd	Benign	20
Dann	Uncertain	0.99
Eigen	Benign	-0.26
Eigen_PC	Benign	-0.090
FATHMM_MKL	Benign	0.043	N
LIST_S2	Benign	0.61	T;T;T
M_CAP	Benign	0.0055	T
MetaRNN	Benign	0.15	T;T;T
MetaSVM	Benign	-1.1	T
MutationTaster	Benign	0.71	P;P;P
PrimateAI	Uncertain	0.52	T
PROVEAN	Benign	-0.48	N;N;N
REVEL	Benign	0.078
Sift	Benign	0.18	T;T;T
Sift4G	Benign	0.51	T;T;T
Polyphen		0.099	.;B;.
Vest4		0.33
MutPred		0.37		Gain of solvent accessibility (P = 0.0145);Gain of solvent accessibility (P = 0.0145);.;
MVP		0.48
MPC		0.21
ClinPred		0.61	D
GERP RS		5.0
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1
Varity_R		0.24
gMVP		0.39

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

Other links and lift over

dbSNP: rs687513; hg19: chr1-100598867;