rs17179360

Variant names:

• chr8-12985053-T-A
• rs17179360
• NM_020844.3:c.-199-5781T>A

Your query was ambiguous. Multiple possible variants found:

• chr8-12985053-T-A
• chr8-12985053-T-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.-199-5781T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.324 in 151,762 control chromosomes in the GnomAD database, including 8,603 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 0.32 (8603 hom., cov: 30)
• Consequence: TRMT9B NM_020844.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.14
• 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=-0.84).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.44 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.-199-5781T>A		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.-199-5781T>A		intron	N/A	ENSP00000432695.1
	TRMT9B	ENST00000447063.6	TSL:2	c.-199-5781T>A		intron	N/A	ENSP00000443288.1
	TRMT9B	ENST00000400069.7	TSL:2	c.-168-5781T>A		intron	N/A	ENSP00000468715.1

Frequencies

GnomAD3 genomes AF: 0.325 AC: 49210 AN: 151644 Hom.: 8604 Cov.: 30

Gnomad AFR AF: 0.213

Gnomad AMI AF: 0.659

Gnomad AMR AF: 0.275

Gnomad ASJ AF: 0.521

Gnomad EAS AF: 0.149

Gnomad SAS AF: 0.457

Gnomad FIN AF: 0.355

Gnomad MID AF: 0.513

Gnomad NFE AF: 0.386

Gnomad OTH AF: 0.352

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

GnomAD4 genome AF: 0.324 AC: 49216 AN: 151762 Hom.: 8603 Cov.: 30 AF XY: 0.323 AC XY: 23974 AN XY: 74122

African (AFR) AF: 0.213 AC: 8832 AN: 41388

American (AMR) AF: 0.274 AC: 4179 AN: 15226

Ashkenazi Jewish (ASJ) AF: 0.521 AC: 1805 AN: 3466

East Asian (EAS) AF: 0.149 AC: 767 AN: 5154

South Asian (SAS) AF: 0.456 AC: 2186 AN: 4792

European-Finnish (FIN) AF: 0.355 AC: 3728 AN: 10490

Middle Eastern (MID) AF: 0.514 AC: 150 AN: 292

European-Non Finnish (NFE) AF: 0.386 AC: 26231 AN: 67928

Other (OTH) AF: 0.349 AC: 738 AN: 2116

Alfa AF: 0.335 Hom.: 1106

Bravo AF: 0.311

Asia WGS AF: 0.292 AC: 1020 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	4.0
DANN	Benign	0.63
PhyloP100		1.1
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: rs17179360; hg19: chr8-12842562;