rs9644018

Variant names:

• chr8-13005073-G-A
• rs9644018
• NM_020844.3:c.-1-1129G>A

Your query was ambiguous. Multiple possible variants found:

• chr8-13005073-G-A
• chr8-13005073-G-C

Variant summary

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

The NM_020844.3(TRMT9B):​c.-1-1129G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.237 in 146,630 control chromosomes in the GnomAD database, including 4,983 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 0.24 (4983 hom., cov: 27)
• Consequence: TRMT9B NM_020844.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.252
• Publications: 2 publications found

Genes affected

TRMT9B (HGNC:26725): (tRNA methyltransferase 9B (putative)) Enables tRNA methyltransferase activity. Predicted to be involved in tRNA wobble uridine modification. Predicted to be active in cytoplasm and nucleus. [provided by Alliance of Genome Resources, Apr 2022]

LOC124901889 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.556 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TRMT9B	NM_020844.3	c.-1-1129G>A		intron_variant	Intron 2 of 4	ENST00000524591.7	NP_065895.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TRMT9B	ENST00000524591.7	c.-1-1129G>A		intron_variant	Intron 2 of 4	5	NM_020844.3	ENSP00000432695.1

Frequencies

GnomAD3 genomes AF: 0.237 AC: 34700 AN: 146552 Hom.: 4973 Cov.: 27

Gnomad AFR AF: 0.109

Gnomad AMI AF: 0.220

Gnomad AMR AF: 0.404

Gnomad ASJ AF: 0.179

Gnomad EAS AF: 0.574

Gnomad SAS AF: 0.159

Gnomad FIN AF: 0.225

Gnomad MID AF: 0.175

Gnomad NFE AF: 0.258

Gnomad OTH AF: 0.258

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

GnomAD4 genome AF: 0.237 AC: 34723 AN: 146630 Hom.: 4983 Cov.: 27 AF XY: 0.238 AC XY: 16959 AN XY: 71180

African (AFR) AF: 0.109 AC: 4236 AN: 38878

American (AMR) AF: 0.405 AC: 5973 AN: 14750

Ashkenazi Jewish (ASJ) AF: 0.179 AC: 617 AN: 3444

East Asian (EAS) AF: 0.573 AC: 2887 AN: 5036

South Asian (SAS) AF: 0.160 AC: 740 AN: 4628

European-Finnish (FIN) AF: 0.225 AC: 2101 AN: 9330

Middle Eastern (MID) AF: 0.180 AC: 51 AN: 284

European-Non Finnish (NFE) AF: 0.258 AC: 17385 AN: 67336

Other (OTH) AF: 0.262 AC: 534 AN: 2040

Alfa AF: 0.239 Hom.: 626

Bravo AF: 0.245

Asia WGS AF: 0.346 AC: 1198 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.8
DANN	Benign	0.35
PhyloP100		0.25
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: rs9644018; hg19: chr8-12862582;