GeneBe

rs9375427

Variant names:

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000648977.1(TRMT11):​n.*1824-6645G>T variant causes a intron 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

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.247

Publications

4 publications found
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]

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -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 HGVSp Effect Exon rank MANE Protein UniProt
TRMT11XR_007059289.1 linkn.1778-6645G>T intron_variant Intron 17 of 17
TRMT11XR_007059290.1 linkn.2031-6645G>T intron_variant Intron 19 of 19
TRMT11XR_007059291.1 linkn.1493-6645G>T intron_variant Intron 13 of 13

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
TRMT11ENST00000648977.1 linkn.*1824-6645G>T intron_variant Intron 21 of 22 ENSP00000496820.1 K7ENP1

Frequencies

GnomAD3 genomes
AF:
0.208
AC:
31625
AN:
151830
Hom.:
3416
Cov.:
32
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.:
32
AF XY:
0.201
AC XY:
14898
AN XY:
74242
show subpopulations
African (AFR)
AF:
0.211
AC:
8732
AN:
41436
American (AMR)
AF:
0.176
AC:
2687
AN:
15284
Ashkenazi Jewish (ASJ)
AF:
0.252
AC:
874
AN:
3468
East Asian (EAS)
AF:
0.0747
AC:
386
AN:
5170
South Asian (SAS)
AF:
0.0880
AC:
423
AN:
4806
European-Finnish (FIN)
AF:
0.161
AC:
1698
AN:
10560
Middle Eastern (MID)
AF:
0.272
AC:
80
AN:
294
European-Non Finnish (NFE)
AF:
0.237
AC:
16106
AN:
67904
Other (OTH)
AF:
0.215
AC:
455
AN:
2114
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.502
Heterozygous variant carriers
0
1264
2529
3793
5058
6322
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
342
684
1026
1368
1710
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
Alfa
AF:
0.223
Hom.:
6830
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
PhyloP100
0.25

Splicing

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

Publications

Other links and lift over

dbSNP: rs9375427; hg19: chr6-126489326; COSMIC: COSV60279800; API