chr8-12962330-T-C

Variant names:

• chr8-12962330-T-C
• rs2203837
• NM_020844.3:c.-200+16364T>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.-200+16364T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.413 in 152,102 control chromosomes in the GnomAD database, including 13,829 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 0.41 (13829 hom., cov: 33)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: TRMT9B NM_020844.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0690
• Publications: 5 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]

ENSG00000251468 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.499 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TRMT9B	NM_020844.3	MANE Select	c.-200+16364T>C		intron	N/A	NP_065895.2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TRMT9B	ENST00000524591.7	TSL:5 MANE Select	c.-200+16364T>C		intron	N/A	ENSP00000432695.1
	TRMT9B	ENST00000855797.1		c.-200+9972T>C		intron	N/A	ENSP00000525856.1
	TRMT9B	ENST00000966194.1		c.-313+9972T>C		intron	N/A	ENSP00000636253.1

Frequencies

GnomAD3 genomes AF: 0.413 AC: 62827 AN: 151984 Hom.: 13814 Cov.: 33

Gnomad AFR AF: 0.308

Gnomad AMI AF: 0.644

Gnomad AMR AF: 0.328

Gnomad ASJ AF: 0.547

Gnomad EAS AF: 0.0931

Gnomad SAS AF: 0.481

Gnomad FIN AF: 0.425

Gnomad MID AF: 0.598

Gnomad NFE AF: 0.503

Gnomad OTH AF: 0.443

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 2 Hom.: 0 AF XY: 0.00 AC XY: 0 AN XY: 2

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 2

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.413 AC: 62865 AN: 152102 Hom.: 13829 Cov.: 33 AF XY: 0.410 AC XY: 30454 AN XY: 74356

African (AFR) AF: 0.308 AC: 12778 AN: 41494

American (AMR) AF: 0.328 AC: 5011 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.547 AC: 1899 AN: 3470

East Asian (EAS) AF: 0.0925 AC: 480 AN: 5188

South Asian (SAS) AF: 0.481 AC: 2317 AN: 4820

European-Finnish (FIN) AF: 0.425 AC: 4486 AN: 10548

Middle Eastern (MID) AF: 0.585 AC: 172 AN: 294

European-Non Finnish (NFE) AF: 0.503 AC: 34205 AN: 67978

Other (OTH) AF: 0.440 AC: 930 AN: 2114

Alfa AF: 0.426 Hom.: 2746

Bravo AF: 0.397

Asia WGS AF: 0.300 AC: 1049 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.8
DANN	Benign	0.41
PhyloP100		0.069
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: rs2203837; hg19: chr8-12819839;