ENST00000718443.1:n.*3349T>A

Variant names:

• chr9-97895438-A-T
• rs7036589
• ENST00000718443.1:n.*3349T>A

Variant summary

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

The ENST00000718443.1(TRMO):​n.*3349T>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.725 in 151,898 control chromosomes in the GnomAD database, including 41,329 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 0.73 (41329 hom., cov: 30)
• Consequence: TRMO ENST00000718443.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.625
• Publications: 6 publications found

Genes affected

TRMO (HGNC:30967): (tRNA methyltransferase O) Enables tRNA (adenine-N6-)-methyltransferase activity. 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 = 0.911 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TRMO	ENST00000718443.1	n.*3349T>A		non_coding_transcript_exon_variant	Exon 6 of 6			ENSP00000520829.1
TRMO	ENST00000718443.1	n.*3349T>A		3_prime_UTR_variant	Exon 6 of 6			ENSP00000520829.1

Frequencies

GnomAD3 genomes AF: 0.725 AC: 110088 AN: 151780 Hom.: 41277 Cov.: 30

Gnomad AFR AF: 0.919

Gnomad AMI AF: 0.426

Gnomad AMR AF: 0.692

Gnomad ASJ AF: 0.610

Gnomad EAS AF: 0.920

Gnomad SAS AF: 0.671

Gnomad FIN AF: 0.648

Gnomad MID AF: 0.690

Gnomad NFE AF: 0.626

Gnomad OTH AF: 0.709

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

GnomAD4 genome AF: 0.725 AC: 110190 AN: 151898 Hom.: 41329 Cov.: 30 AF XY: 0.728 AC XY: 53996 AN XY: 74220

African (AFR) AF: 0.919 AC: 38122 AN: 41472

American (AMR) AF: 0.692 AC: 10557 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.610 AC: 2117 AN: 3470

East Asian (EAS) AF: 0.921 AC: 4761 AN: 5170

South Asian (SAS) AF: 0.670 AC: 3213 AN: 4794

European-Finnish (FIN) AF: 0.648 AC: 6819 AN: 10518

Middle Eastern (MID) AF: 0.697 AC: 205 AN: 294

European-Non Finnish (NFE) AF: 0.626 AC: 42519 AN: 67914

Other (OTH) AF: 0.707 AC: 1490 AN: 2108

Alfa AF: 0.683 Hom.: 4539

Bravo AF: 0.739

Asia WGS AF: 0.781 AC: 2718 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.5
DANN	Benign	0.57
PhyloP100		-0.63

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs7036589; hg19: chr9-100657720;