rs687513

Variant names:

• chr1-100133311-C-A
• rs687513
• NM_019083.3:c.143C>A

Your query was ambiguous. Multiple possible variants found:

• chr1-100133311-C-A
• chr1-100133311-C-T

Variant summary

Our verdict is Uncertain significance. The variant received 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. 14/22 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. A48V) 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
• Publications: 26 publications found

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

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

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

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_019083.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TRMT13	NM_019083.3	MANE Select	c.143C>A	p.Ala48Glu	missense	Exon 1 of 11	NP_061956.2	Q9NUP7-1
	TRMT13	NM_001393409.1		c.143C>A	p.Ala48Glu	missense	Exon 1 of 11	NP_001380338.1
	TRMT13	NM_001393410.1		c.143C>A	p.Ala48Glu	missense	Exon 1 of 9	NP_001380339.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TRMT13	ENST00000370141.8	TSL:1 MANE Select	c.143C>A	p.Ala48Glu	missense	Exon 1 of 11	ENSP00000359160.2	Q9NUP7-1
	TRMT13	ENST00000962881.1		c.143C>A	p.Ala48Glu	missense	Exon 1 of 11	ENSP00000632940.1
	TRMT13	ENST00000370139.1	TSL:3	c.50C>A	p.Ala17Glu	missense	Exon 1 of 6	ENSP00000359158.1	Q5VVK9

Frequencies

GnomAD3 genomes Cov.: 30

GnomAD4 exome Cov.: 54

GnomAD4 genome Cov.: 30

Alfa AF: 0.00 Hom.: 157722

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

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
DEOGEN2	Benign	0.017	T
Eigen	Benign	-0.26
Eigen_PC	Benign	-0.090
FATHMM_MKL	Benign	0.043	N
LIST_S2	Benign	0.61	T
M_CAP	Benign	0.0055	T
MetaRNN	Benign	0.15	T
MetaSVM	Benign	-1.1	T
MutationAssessor	Benign	0.77	N
PhyloP100		1.5
PrimateAI	Uncertain	0.52	T
PROVEAN	Benign	-0.48	N
REVEL	Benign	0.078
Sift	Benign	0.18	T
Sift4G	Benign	0.51	T
Polyphen		0.099	B
Vest4		0.33
MutPred		0.37		Gain of solvent accessibility (P = 0.0145)
MVP		0.48
MPC		0.21
ClinPred		0.61	D
GERP RS		5.0
PromoterAI		-0.042	Neutral
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1
Varity_R		0.24
gMVP		0.39
Mutation Taster		=79/21	polymorphism

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

Other links and lift over

dbSNP: rs687513; hg19: chr1-100598867;