9-97910060-GC-AT

Variant names:

• chr9-97910060-GC-AT
• NM_016481.5:c.965_966delGCinsAT
• TRMO p.Arg322His

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.

The NM_016481.5(TRMO):​c.965_966delGCinsAT​(p.Arg322His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. It is difficult to determine the true allele frequency of this variant because it is of type MNV, and the frequency of such variant types in population databases may be underestimated and unreliable. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another nucleotide change resulting in the same amino acid substitution has been previously reported as Likely benign in ClinVar.

• Frequency: Genomes: not found (cov: 32)
• Consequence: TRMO NM_016481.5 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.28
• Publications: 0 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: Uncertain_significance. The variant received 0 ACMG points.

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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TRMO	NM_016481.5	MANE Select	c.965_966delGCinsAT	p.Arg322His	missense	N/A	NP_057565.3
	TRMO	NM_001371657.1		c.965_966delGCinsAT	p.Arg322His	missense	N/A	NP_001358586.1	Q9BU70
	TRMO	NM_001371658.1		c.965_966delGCinsAT	p.Arg322His	missense	N/A	NP_001358587.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TRMO	ENST00000375119.8	TSL:1 MANE Select	c.965_966delGCinsAT	p.Arg322His	missense	N/A	ENSP00000364260.3	Q9BU70
	TRMO	ENST00000375118.1	TSL:1	c.527_528delGCinsAT	p.Arg176His	missense	N/A	ENSP00000364259.1	Q5T114
	TRMO	ENST00000864009.1		c.965_966delGCinsAT	p.Arg322His	missense	N/A	ENSP00000534068.1

Frequencies

GnomAD3 genomes Cov.: 32

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

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		3.3

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

hg19: chr9-100672342;