chr1-100148662-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_019083.3(TRMT13):c.1288C>T(p.Leu430Phe) variant causes a missense change. The variant allele was found at a frequency of 0.0000205 in 1,611,456 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. L430I) has been classified as Uncertain significance.
Frequency
Consequence
NM_019083.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TRMT13 | NM_019083.3 | c.1288C>T | p.Leu430Phe | missense_variant | 11/11 | ENST00000370141.8 | |
LRRC39 | NM_144620.4 | c.*380G>A | 3_prime_UTR_variant | 10/10 | ENST00000370137.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TRMT13 | ENST00000370141.8 | c.1288C>T | p.Leu430Phe | missense_variant | 11/11 | 1 | NM_019083.3 | P1 | |
LRRC39 | ENST00000370137.6 | c.*380G>A | 3_prime_UTR_variant | 10/10 | 1 | NM_144620.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000263 AC: 4AN: 152152Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000523 AC: 13AN: 248732Hom.: 0 AF XY: 0.0000521 AC XY: 7AN XY: 134362
GnomAD4 exome AF: 0.0000199 AC: 29AN: 1459304Hom.: 0 Cov.: 31 AF XY: 0.0000165 AC XY: 12AN XY: 725768
GnomAD4 genome ? AF: 0.0000263 AC: 4AN: 152152Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74326
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 13, 2021 | The c.1288C>T (p.L430F) alteration is located in exon 11 (coding exon 11) of the TRMT13 gene. This alteration results from a C to T substitution at nucleotide position 1288, causing the leucine (L) at amino acid position 430 to be replaced by a phenylalanine (F). 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