chr1-185120198-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_030934.5(TRMT1L):c.2023G>A(p.Val675Ile) variant causes a missense change. The variant allele was found at a frequency of 0.00000558 in 1,612,802 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict 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 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TRMT1L | NM_030934.5 | c.2023G>A | p.Val675Ile | missense_variant | Exon 15 of 15 | ENST00000367506.10 | NP_112196.3 | |
TRMT1L | NM_001202423.2 | c.1555G>A | p.Val519Ile | missense_variant | Exon 15 of 15 | NP_001189352.1 | ||
TRMT1L | XM_047431291.1 | c.1555G>A | p.Val519Ile | missense_variant | Exon 15 of 15 | XP_047287247.1 | ||
TRMT1L | XM_047431292.1 | c.1555G>A | p.Val519Ile | missense_variant | Exon 15 of 15 | XP_047287248.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152152Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000199 AC: 5AN: 251170Hom.: 0 AF XY: 0.0000147 AC XY: 2AN XY: 135756
GnomAD4 exome AF: 0.00000548 AC: 8AN: 1460650Hom.: 0 Cov.: 31 AF XY: 0.00000413 AC XY: 3AN XY: 726684
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152152Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74330
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.2023G>A (p.V675I) alteration is located in exon 15 (coding exon 15) of the TRMT1L gene. This alteration results from a G to A substitution at nucleotide position 2023, causing the valine (V) at amino acid position 675 to be replaced by an isoleucine (I). 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