1-100146015-C-T

Variant names:

• chr1-100146015-C-T
• rs12733952
• NM_019083.3:c.817+1872C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_019083.3(TRMT13):​c.817+1872C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.749 in 152,180 control chromosomes in the GnomAD database, including 45,367 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 0.75 (45367 hom., cov: 31)
• Consequence: TRMT13 NM_019083.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.832
• Publications: 6 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: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.923 is higher than 0.05.

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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TRMT13	NM_019083.3	MANE Select	c.817+1872C>T		intron	N/A	NP_061956.2
	TRMT13	NM_001393409.1		c.775+1872C>T		intron	N/A	NP_001380338.1
	TRMT13	NM_001393410.1		c.703+1872C>T		intron	N/A	NP_001380339.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TRMT13	ENST00000370141.8	TSL:1 MANE Select	c.817+1872C>T		intron	N/A	ENSP00000359160.2

Frequencies

GnomAD3 genomes AF: 0.749 AC: 113970 AN: 152062 Hom.: 45355 Cov.: 31

Gnomad AFR AF: 0.452

Gnomad AMI AF: 0.804

Gnomad AMR AF: 0.852

Gnomad ASJ AF: 0.890

Gnomad EAS AF: 0.945

Gnomad SAS AF: 0.896

Gnomad FIN AF: 0.886

Gnomad MID AF: 0.854

Gnomad NFE AF: 0.851

Gnomad OTH AF: 0.784

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.749 AC: 114009 AN: 152180 Hom.: 45367 Cov.: 31 AF XY: 0.756 AC XY: 56235 AN XY: 74414

African (AFR) AF: 0.452 AC: 18734 AN: 41476

American (AMR) AF: 0.852 AC: 13037 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.890 AC: 3089 AN: 3470

East Asian (EAS) AF: 0.945 AC: 4902 AN: 5188

South Asian (SAS) AF: 0.896 AC: 4329 AN: 4832

European-Finnish (FIN) AF: 0.886 AC: 9398 AN: 10602

Middle Eastern (MID) AF: 0.864 AC: 254 AN: 294

European-Non Finnish (NFE) AF: 0.851 AC: 57872 AN: 68002

Other (OTH) AF: 0.787 AC: 1661 AN: 2110

Alfa AF: 0.790 Hom.: 9249

Bravo AF: 0.735

Asia WGS AF: 0.869 AC: 3021 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.4
DANN	Benign	0.66
PhyloP100		-0.83
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.0
Mutation Taster		=100/0	polymorphism (auto)

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: rs12733952; hg19: chr1-100611571;