rs17179360

Positions:

• chr8-12985053-T-A
• chr8-12985053-T-C

Variant summary

Our verdict is Benign. Variant got -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

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=-0.84).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.44 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TRMT9B	NM_020844.3	c.-199-5781T>A		intron_variant		ENST00000524591.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TRMT9B	ENST00000524591.7	c.-199-5781T>A		intron_variant		5	NM_020844.3	P1

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

Gnomad4 AFR AF: 0.213

Gnomad4 AMR AF: 0.274

Gnomad4 ASJ AF: 0.521

Gnomad4 EAS AF: 0.149

Gnomad4 SAS AF: 0.456

Gnomad4 FIN AF: 0.355

Gnomad4 NFE AF: 0.386

Gnomad4 OTH AF: 0.349

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 v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	4.0
DANN	Benign	0.63

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: rs17179360; hg19: chr8-12842562;