rs1569741

Variant summary

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

The XR_007059300.1(TRMT11):​n.4255G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.57 in 152,126 control chromosomes in the GnomAD database, including 26,385 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 0.57 ( 26385 hom., cov: 33)

Consequence

TRMT11
XR_007059300.1 non_coding_transcript_exon

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.746
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]

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=-0.9).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.897 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
TRMT11XR_007059300.1 linkuse as main transcriptn.4255G>A non_coding_transcript_exon_variant 15/16
TRMT11XR_007059315.1 linkuse as main transcriptn.4204G>A non_coding_transcript_exon_variant 14/15
TRMT11XR_007059316.1 linkuse as main transcriptn.4388G>A non_coding_transcript_exon_variant 17/19

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
TRMT11ENST00000648977.1 linkuse as main transcriptc.*1437+9140G>A intron_variant, NMD_transcript_variant ENSP00000496820

Frequencies

GnomAD3 genomes
AF:
0.569
AC:
86528
AN:
152008
Hom.:
26329
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.734
Gnomad AMI
AF:
0.238
Gnomad AMR
AF:
0.634
Gnomad ASJ
AF:
0.391
Gnomad EAS
AF:
0.919
Gnomad SAS
AF:
0.605
Gnomad FIN
AF:
0.574
Gnomad MID
AF:
0.484
Gnomad NFE
AF:
0.439
Gnomad OTH
AF:
0.539
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.570
AC:
86650
AN:
152126
Hom.:
26385
Cov.:
33
AF XY:
0.578
AC XY:
42968
AN XY:
74368
show subpopulations
Gnomad4 AFR
AF:
0.734
Gnomad4 AMR
AF:
0.635
Gnomad4 ASJ
AF:
0.391
Gnomad4 EAS
AF:
0.919
Gnomad4 SAS
AF:
0.604
Gnomad4 FIN
AF:
0.574
Gnomad4 NFE
AF:
0.439
Gnomad4 OTH
AF:
0.543
Alfa
AF:
0.460
Hom.:
7966
Bravo
AF:
0.584
Asia WGS
AF:
0.742
AC:
2576
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.90
CADD
Benign
0.16
DANN
Benign
0.61

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.

Other links and lift over

dbSNP: rs1569741; hg19: chr6-126383476; API