9-97904649-C-A

Variant names:

• chr9-97904649-C-A
• rs6586
• NM_016481.5:c.*84G>T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_016481.5(TRMO):​c.*84G>T variant causes a 3 prime UTR 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. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: not found (cov: 32)
• Consequence: TRMO NM_016481.5 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.19
• Publications: 37 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: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_016481.5. 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
	TRMO	NM_016481.5	MANE Select	c.*84G>T		3_prime_UTR	Exon 5 of 5	NP_057565.3
	TRMO	NM_001371659.1		c.*84G>T		3_prime_UTR	Exon 5 of 5	NP_001358588.1
	TRMO	NM_001330725.2		c.*84G>T		3_prime_UTR	Exon 6 of 6	NP_001317654.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TRMO	ENST00000375119.8	TSL:1 MANE Select	c.*84G>T		3_prime_UTR	Exon 5 of 5	ENSP00000364260.3
	TRMO	ENST00000375118.1	TSL:1	c.*84G>T		3_prime_UTR	Exon 2 of 2	ENSP00000364259.1
	TRMO	ENST00000718443.1		n.1067-3816G>T		intron	N/A	ENSP00000520829.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 36

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	3.2
DANN	Benign	0.75
PhyloP100		-1.2

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: rs6586; hg19: chr9-100666931;