1-185137684-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_030934.5(TRMT1L):c.1435G>A(p.Ala479Thr) variant causes a missense change. The variant allele was found at a frequency of 0.00000137 in 1,461,830 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_030934.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TRMT1L | NM_030934.5 | c.1435G>A | p.Ala479Thr | missense_variant | Exon 10 of 15 | ENST00000367506.10 | NP_112196.3 | |
TRMT1L | NM_001202423.2 | c.967G>A | p.Ala323Thr | missense_variant | Exon 10 of 15 | NP_001189352.1 | ||
TRMT1L | XM_047431291.1 | c.967G>A | p.Ala323Thr | missense_variant | Exon 10 of 15 | XP_047287247.1 | ||
TRMT1L | XM_047431292.1 | c.967G>A | p.Ala323Thr | missense_variant | Exon 10 of 15 | XP_047287248.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TRMT1L | ENST00000367506.10 | c.1435G>A | p.Ala479Thr | missense_variant | Exon 10 of 15 | 1 | NM_030934.5 | ENSP00000356476.5 | ||
TRMT1L | ENST00000458395.1 | c.307G>A | p.Ala103Thr | missense_variant | Exon 2 of 4 | 3 | ENSP00000414339.1 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.00000398 AC: 1AN: 251062Hom.: 0 AF XY: 0.00000737 AC XY: 1AN XY: 135668
GnomAD4 exome AF: 0.00000137 AC: 2AN: 1461830Hom.: 0 Cov.: 31 AF XY: 0.00000275 AC XY: 2AN XY: 727216
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1435G>A (p.A479T) alteration is located in exon 10 (coding exon 10) of the TRMT1L gene. This alteration results from a G to A substitution at nucleotide position 1435, causing the alanine (A) at amino acid position 479 to be replaced by a threonine (T). 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