rs2203836

Variant names:

• chr8-12967279-G-C
• rs2203836
• NM_020844.3:c.-200+21313G>C

Your query was ambiguous. Multiple possible variants found:

• chr8-12967279-G-C
• chr8-12967279-G-T

Variant summary

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

The NM_020844.3(TRMT9B):​c.-200+21313G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.796 in 152,146 control chromosomes in the GnomAD database, including 48,244 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 0.80 (48244 hom., cov: 32)
• Consequence: TRMT9B NM_020844.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.691
• Publications: 1 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]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.805 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_020844.3. 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
	TRMT9B	NM_020844.3	MANE Select	c.-200+21313G>C		intron	N/A	NP_065895.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TRMT9B	ENST00000524591.7	TSL:5 MANE Select	c.-200+21313G>C		intron	N/A	ENSP00000432695.1
	TRMT9B	ENST00000447063.6	TSL:2	c.-200+21313G>C		intron	N/A	ENSP00000443288.1
	TRMT9B	ENST00000400069.7	TSL:2	c.-169+14921G>C		intron	N/A	ENSP00000468715.1

Frequencies

GnomAD3 genomes AF: 0.796 AC: 120967 AN: 152028 Hom.: 48210 Cov.: 32

Gnomad AFR AF: 0.803

Gnomad AMI AF: 0.872

Gnomad AMR AF: 0.816

Gnomad ASJ AF: 0.833

Gnomad EAS AF: 0.736

Gnomad SAS AF: 0.685

Gnomad FIN AF: 0.756

Gnomad MID AF: 0.883

Gnomad NFE AF: 0.801

Gnomad OTH AF: 0.815

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

GnomAD4 genome AF: 0.796 AC: 121059 AN: 152146 Hom.: 48244 Cov.: 32 AF XY: 0.792 AC XY: 58899 AN XY: 74376

African (AFR) AF: 0.803 AC: 33337 AN: 41494

American (AMR) AF: 0.817 AC: 12478 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.833 AC: 2892 AN: 3472

East Asian (EAS) AF: 0.735 AC: 3789 AN: 5156

South Asian (SAS) AF: 0.685 AC: 3305 AN: 4826

European-Finnish (FIN) AF: 0.756 AC: 7999 AN: 10578

Middle Eastern (MID) AF: 0.888 AC: 261 AN: 294

European-Non Finnish (NFE) AF: 0.801 AC: 54484 AN: 68018

Other (OTH) AF: 0.813 AC: 1719 AN: 2114

Alfa AF: 0.740 Hom.: 2492

Bravo AF: 0.805

Asia WGS AF: 0.714 AC: 2484 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.31
DANN	Benign	0.65
PhyloP100		-0.69
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: rs2203836; hg19: chr8-12824788;