Variant rs9375427 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000648977.1(TRMT11):c.*1824-6645G>T variant causes a intron, NMD transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.208 in 151,948 control chromosomes in the GnomAD database, including 3,413 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 0.21 ( 3413 hom., cov: 32)

Consequence

TRMT11
ENST00000648977.1 intron, NMD_transcript

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.247

Variant links:

Genes affected

TRMT11 (HGNC:21080): (tRNA methyltransferase 11 homolog) Predicted to enable tRNA (guanine-N2-)-methyltransferase activity. Predicted to be involved in tRNA methylation. Predicted to be active in cytoplasm. [provided by Alliance of Genome Resources, Apr 2022]

TRMT11 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.83).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.234 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect
TRMT11	XR_007059289.1 linkuse as main transcript	n.1778-6645G>T	intron_variant, non_coding_transcript_variant
TRMT11	XR_007059290.1 linkuse as main transcript	n.2031-6645G>T	intron_variant, non_coding_transcript_variant
TRMT11	XR_007059291.1 linkuse as main transcript	n.1493-6645G>T	intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TRMT11	ENST00000648977.1 linkuse as main transcript	c.*1824-6645G>T		intron_variant, NMD_transcript_variant				ENSP00000496820

Frequencies

GnomAD3 genomes

AF:

0.208

AC:

31625

AN:

151830

Hom.:

3416

Cov.:

show subpopulations

Gnomad AFR

AF:

0.211

Gnomad AMI

AF:

0.217

Gnomad AMR

AF:

0.176

Gnomad ASJ

AF:

0.252

Gnomad EAS

AF:

0.0745

Gnomad SAS

AF:

0.0871

Gnomad FIN

AF:

0.161

Gnomad MID

AF:

0.269

Gnomad NFE

AF:

0.237

Gnomad OTH

AF:

0.217

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

GnomAD4 genome

AF:

0.208

AC:

31639

AN:

151948

Hom.:

3413

Cov.:

AF XY:

0.201

AC XY:

14898

AN XY:

74242

show subpopulations

Gnomad4 AFR

AF:

0.211

Gnomad4 AMR

AF:

0.176

Gnomad4 ASJ

AF:

0.252

Gnomad4 EAS

AF:

0.0747

Gnomad4 SAS

AF:

0.0880

Gnomad4 FIN

AF:

0.161

Gnomad4 NFE

AF:

0.237

Gnomad4 OTH

AF:

0.215

Alfa

AF:

0.222

Hom.:

2061

Bravo

AF:

0.210

Asia WGS

AF:

0.0890

AC:

310

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.83

CADD

Benign

2.9

DANN

Benign

0.37

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over