chr14-60975158-G-A
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 2P and 12B. PM2BP4_StrongBP6_Very_Strong
The NM_020810.3(TRMT5):c.1481C>T(p.Thr494Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000284 in 1,607,240 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 11/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★). Synonymous variant affecting the same amino acid position (i.e. T494T) has been classified as Likely benign.
Frequency
Consequence
NM_020810.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TRMT5 | NM_020810.3 | c.1481C>T | p.Thr494Met | missense_variant | 5/5 | ENST00000261249.7 | |
TRMT5 | NM_001350253.1 | c.1565C>T | p.Thr522Met | missense_variant | 5/5 | ||
TRMT5 | NM_001350254.1 | c.1562C>T | p.Thr521Met | missense_variant | 5/5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TRMT5 | ENST00000261249.7 | c.1481C>T | p.Thr494Met | missense_variant | 5/5 | 1 | NM_020810.3 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000454 AC: 69AN: 152050Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000732 AC: 180AN: 246018Hom.: 0 AF XY: 0.000736 AC XY: 98AN XY: 133176
GnomAD4 exome AF: 0.000266 AC: 387AN: 1455072Hom.: 0 Cov.: 30 AF XY: 0.000298 AC XY: 216AN XY: 723794
GnomAD4 genome AF: 0.000453 AC: 69AN: 152168Hom.: 0 Cov.: 32 AF XY: 0.000551 AC XY: 41AN XY: 74380
ClinVar
Submissions by phenotype
Combined oxidative phosphorylation defect type 26 Uncertain:1
Uncertain significance, no assertion criteria provided | clinical testing | Institute of Pediatric Research, Children's Hospital of Soochow University, Soochow University | - | - - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 02, 2024 | - - |
TRMT5-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Jan 27, 2020 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at