8-124451208-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_017956.4(TRMT12):c.281C>T(p.Pro94Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000062 in 1,614,120 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_017956.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TRMT12 | ENST00000328599.4 | c.281C>T | p.Pro94Leu | missense_variant | Exon 1 of 1 | 6 | NM_017956.4 | ENSP00000329858.3 | ||
TRMT12 | ENST00000521443.1 | n.389C>T | non_coding_transcript_exon_variant | Exon 1 of 2 | 4 | |||||
TRMT12 | ENST00000522518.1 | n.281C>T | non_coding_transcript_exon_variant | Exon 1 of 3 | 3 | ENSP00000429771.1 |
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152112Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000398 AC: 1AN: 250972Hom.: 0 AF XY: 0.00000737 AC XY: 1AN XY: 135640
GnomAD4 exome AF: 0.00000479 AC: 7AN: 1461890Hom.: 0 Cov.: 41 AF XY: 0.00000275 AC XY: 2AN XY: 727248
GnomAD4 genome AF: 0.0000197 AC: 3AN: 152230Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74426
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.281C>T (p.P94L) alteration is located in exon 1 (coding exon 1) of the TRMT12 gene. This alteration results from a C to T substitution at nucleotide position 281, causing the proline (P) at amino acid position 94 to be replaced by a leucine (L). 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