rs2977097

chr8-12946592-G-Achr8-12946592-G-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+626G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.301 in 152,034 control chromosomes in the GnomAD database, including 7,204 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 0.30 (7204 hom., cov: 32)
• Consequence: TRMT9B NM_020844.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.808

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=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.504 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TRMT9B	NM_020844.3	c.-200+626G>A		intron_variant		ENST00000524591.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TRMT9B	ENST00000524591.7	c.-200+626G>A		intron_variant		5	NM_020844.3	P1
TRMT9B	ENST00000447063.6	c.-200+626G>A		intron_variant		2
TRMT9B	ENST00000525249.1	n.293+626G>A		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.301 AC: 45724 AN: 151916 Hom.: 7197 Cov.: 32

Gnomad AFR AF: 0.227

Gnomad AMI AF: 0.171

Gnomad AMR AF: 0.411

Gnomad ASJ AF: 0.277

Gnomad EAS AF: 0.521

Gnomad SAS AF: 0.213

Gnomad FIN AF: 0.330

Gnomad MID AF: 0.272

Gnomad NFE AF: 0.309

Gnomad OTH AF: 0.318

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

GnomAD4 genome AF: 0.301 AC: 45751 AN: 152034 Hom.: 7204 Cov.: 32 AF XY: 0.302 AC XY: 22477 AN XY: 74314

Gnomad4 AFR AF: 0.227

Gnomad4 AMR AF: 0.411

Gnomad4 ASJ AF: 0.277

Gnomad4 EAS AF: 0.520

Gnomad4 SAS AF: 0.213

Gnomad4 FIN AF: 0.330

Gnomad4 NFE AF: 0.309

Gnomad4 OTH AF: 0.321

Alfa AF: 0.315 Hom.: 12843

Bravo AF: 0.308

Asia WGS AF: 0.345 AC: 1198 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
Cadd	Benign	2.4
Dann	Benign	0.76

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: rs2977097; hg19: chr8-12804101;