rs2203834

Positions:

• chr8-12967384-A-C
• chr8-12967384-A-G
• chr8-12967384-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_020844.3(TRMT9B):​c.-200+21418A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.869 in 152,210 control chromosomes in the GnomAD database, including 57,654 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 0.87 (57654 hom., cov: 32)
• Consequence: TRMT9B NM_020844.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.807

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.892 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TRMT9B	NM_020844.3	c.-200+21418A>C		intron_variant		ENST00000524591.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TRMT9B	ENST00000524591.7	c.-200+21418A>C		intron_variant		5	NM_020844.3	P1

Frequencies

GnomAD3 genomes AF: 0.869 AC: 132218 AN: 152092 Hom.: 57604 Cov.: 32

Gnomad AFR AF: 0.899

Gnomad AMI AF: 0.890

Gnomad AMR AF: 0.889

Gnomad ASJ AF: 0.900

Gnomad EAS AF: 0.769

Gnomad SAS AF: 0.786

Gnomad FIN AF: 0.831

Gnomad MID AF: 0.921

Gnomad NFE AF: 0.864

Gnomad OTH AF: 0.876

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

GnomAD4 genome AF: 0.869 AC: 132326 AN: 152210 Hom.: 57654 Cov.: 32 AF XY: 0.866 AC XY: 64387 AN XY: 74390

Gnomad4 AFR AF: 0.899

Gnomad4 AMR AF: 0.889

Gnomad4 ASJ AF: 0.900

Gnomad4 EAS AF: 0.769

Gnomad4 SAS AF: 0.785

Gnomad4 FIN AF: 0.831

Gnomad4 NFE AF: 0.864

Gnomad4 OTH AF: 0.873

Alfa AF: 0.869 Hom.: 74119

Bravo AF: 0.878

Asia WGS AF: 0.766 AC: 2667 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.77
DANN	Benign	0.38

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

Publications

LitVar

Other links and lift over

dbSNP: rs2203834; hg19: chr8-12824893;