rs9644018

Positions:

• chr8-13005073-G-A

Variant summary

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

The NM_020844.3(TRMT9B):​c.-1-1129G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.237 in 146,630 control chromosomes in the GnomAD database, including 4,983 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 0.24 (4983 hom., cov: 27)
• Consequence: TRMT9B NM_020844.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.252

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.556 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TRMT9B	NM_020844.3	c.-1-1129G>A		intron_variant		ENST00000524591.7
LOC124901889	XR_007060825.1	n.491+9267C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TRMT9B	ENST00000524591.7	c.-1-1129G>A		intron_variant		5	NM_020844.3	P1

Frequencies

GnomAD3 genomes AF: 0.237 AC: 34700 AN: 146552 Hom.: 4973 Cov.: 27

Gnomad AFR AF: 0.109

Gnomad AMI AF: 0.220

Gnomad AMR AF: 0.404

Gnomad ASJ AF: 0.179

Gnomad EAS AF: 0.574

Gnomad SAS AF: 0.159

Gnomad FIN AF: 0.225

Gnomad MID AF: 0.175

Gnomad NFE AF: 0.258

Gnomad OTH AF: 0.258

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

GnomAD4 genome AF: 0.237 AC: 34723 AN: 146630 Hom.: 4983 Cov.: 27 AF XY: 0.238 AC XY: 16959 AN XY: 71180

Gnomad4 AFR AF: 0.109

Gnomad4 AMR AF: 0.405

Gnomad4 ASJ AF: 0.179

Gnomad4 EAS AF: 0.573

Gnomad4 SAS AF: 0.160

Gnomad4 FIN AF: 0.225

Gnomad4 NFE AF: 0.258

Gnomad4 OTH AF: 0.262

Alfa AF: 0.239 Hom.: 626

Bravo AF: 0.245

Asia WGS AF: 0.346 AC: 1198 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.8
DANN	Benign	0.35

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: rs9644018; hg19: chr8-12862582;