dbSNP rs13251099: TRMT9B:c.-200+6093A>G (chr8-12952059-A-G) – ACMG Classification: Likely_benign (-2 pts)

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2BP4_Strong

The NM_020844.3(TRMT9B):c.-200+6093A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000603 in 165,900 control chromosomes in the GnomAD database, with no homozygous occurrence. 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: not found (cov: 33)

Exomes 𝑓: 0.0000060 ( 0 hom. )

Consequence

TRMT9B
NM_020844.3 intron

Scores

Splicing: ADA: 0.0002223

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.137

Publications

0 publications found

Variant links:

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]

TRMT9B links:

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ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -2 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.58).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TRMT9B	NM_020844.3 link	c.-200+6093A>G		intron_variant	Intron 1 of 4	ENST00000524591.7	NP_065895.2	Q9P272-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TRMT9B	ENST00000524591.7 link	c.-200+6093A>G		intron_variant	Intron 1 of 4	5	NM_020844.3	ENSP00000432695.1		Q9P272-1

Frequencies

GnomAD3 genomes

Cov.:

GnomAD4 exome

AF:

0.00000603

AC:

AN:

165900

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

94838

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

2960

American (AMR)

AF:

0.00

AC:

AN:

10182

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

4652

East Asian (EAS)

AF:

0.00

AC:

AN:

3624

South Asian (SAS)

AF:

0.00

AC:

AN:

39310

European-Finnish (FIN)

AF:

0.00

AC:

AN:

8694

Middle Eastern (MID)

AF:

0.00

AC:

AN:

2198

European-Non Finnish (NFE)

AF:

0.0000116

AC:

AN:

86490

Other (OTH)

AF:

0.00

AC:

AN:

7790

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.675

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

Cov.:

Alfa

AF:

0.00

Hom.:

Bravo

AF:

0.00000378

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.58

CADD

Benign

(source)

DANN

Benign

0.83

PhyloP100

-0.14

PromoterAI

-0.011

Neutral

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

dbscSNV1_ADA

Benign

0.00022

dbscSNV1_RF

Benign

0.032

SpliceAI score (max)

0.010

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

Other links and lift over