rs7037324

Variant names:

• chr9-97896036-A-G
• rs7037324
• ENST00000718443.1:n.*2751T>C

Your query was ambiguous. Multiple possible variants found:

• chr9-97896036-A-G
• chr9-97896036-A-T

Variant summary

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

The ENST00000718443.1(TRMO):​n.*2751T>C 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 0.711 in 152,014 control chromosomes in the GnomAD database, including 39,413 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 0.71 (39413 hom., cov: 31)
• Consequence: TRMO ENST00000718443.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.06
• Publications: 17 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=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.899 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.*2751T>C		non_coding_transcript_exon_variant	Exon 6 of 6			ENSP00000520829.1
TRMO	ENST00000718443.1	n.*2751T>C		3_prime_UTR_variant	Exon 6 of 6			ENSP00000520829.1

Frequencies

GnomAD3 genomes AF: 0.711 AC: 107967 AN: 151896 Hom.: 39368 Cov.: 31

Gnomad AFR AF: 0.870

Gnomad AMI AF: 0.426

Gnomad AMR AF: 0.686

Gnomad ASJ AF: 0.610

Gnomad EAS AF: 0.920

Gnomad SAS AF: 0.672

Gnomad FIN AF: 0.647

Gnomad MID AF: 0.684

Gnomad NFE AF: 0.625

Gnomad OTH AF: 0.696

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

GnomAD4 genome AF: 0.711 AC: 108057 AN: 152014 Hom.: 39413 Cov.: 31 AF XY: 0.713 AC XY: 52952 AN XY: 74276

African (AFR) AF: 0.870 AC: 36088 AN: 41490

American (AMR) AF: 0.687 AC: 10481 AN: 15266

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

East Asian (EAS) AF: 0.921 AC: 4764 AN: 5174

South Asian (SAS) AF: 0.671 AC: 3236 AN: 4820

European-Finnish (FIN) AF: 0.647 AC: 6823 AN: 10542

Middle Eastern (MID) AF: 0.690 AC: 203 AN: 294

European-Non Finnish (NFE) AF: 0.625 AC: 42492 AN: 67938

Other (OTH) AF: 0.694 AC: 1465 AN: 2110

Alfa AF: 0.670 Hom.: 47933

Bravo AF: 0.723

Asia WGS AF: 0.778 AC: 2708 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	7.2
DANN	Benign	0.67
PhyloP100		1.1

Splicing

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

Other links and lift over

dbSNP: rs7037324; hg19: chr9-100658318;