chr14-60975478-G-C
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_020810.3(TRMT5):āc.1441C>Gā(p.Pro481Ala) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000038 in 1,605,234 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. P481R) has been classified as Uncertain significance.
Frequency
Consequence
NM_020810.3 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TRMT5 | NM_020810.3 | c.1441C>G | p.Pro481Ala | missense_variant | 4/5 | ENST00000261249.7 | |
TRMT5 | NM_001350253.1 | c.1525C>G | p.Pro509Ala | missense_variant | 4/5 | ||
TRMT5 | NM_001350254.1 | c.1522C>G | p.Pro508Ala | missense_variant | 4/5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TRMT5 | ENST00000261249.7 | c.1441C>G | p.Pro481Ala | missense_variant | 4/5 | 1 | NM_020810.3 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152178Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000849 AC: 21AN: 247388Hom.: 0 AF XY: 0.000142 AC XY: 19AN XY: 133790
GnomAD4 exome AF: 0.0000406 AC: 59AN: 1453056Hom.: 0 Cov.: 31 AF XY: 0.0000624 AC XY: 45AN XY: 721458
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152178Hom.: 0 Cov.: 33 AF XY: 0.0000269 AC XY: 2AN XY: 74340
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | May 14, 2024 | The c.1441C>G (p.P481A) alteration is located in exon 4 (coding exon 4) of the TRMT5 gene. This alteration results from a C to G substitution at nucleotide position 1441, causing the proline (P) at amino acid position 481 to be replaced by an alanine (A). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at