1-100133311-C-T
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_019083.3(TRMT13):c.143C>T(p.Ala48Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.839 in 1,612,780 control chromosomes in the GnomAD database, including 574,372 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. A48T) has been classified as Benign.
Frequency
Consequence
NM_019083.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TRMT13 | NM_019083.3 | c.143C>T | p.Ala48Val | missense_variant | 1/11 | ENST00000370141.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TRMT13 | ENST00000370141.8 | c.143C>T | p.Ala48Val | missense_variant | 1/11 | 1 | NM_019083.3 | P1 | |
TRMT13 | ENST00000370139.1 | c.50C>T | p.Ala17Val | missense_variant | 1/6 | 3 | |||
TRMT13 | ENST00000370143.5 | c.143C>T | p.Ala48Val | missense_variant | 1/5 | 3 | |||
TRMT13 | ENST00000482437.5 | c.143C>T | p.Ala48Val | missense_variant, NMD_transcript_variant | 1/8 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.748 AC: 113327AN: 151478Hom.: 45037 Cov.: 30
GnomAD3 exomes AF: 0.851 AC: 212744AN: 250002Hom.: 92100 AF XY: 0.857 AC XY: 115793AN XY: 135118
GnomAD4 exome AF: 0.848 AC: 1239550AN: 1461182Hom.: 529322 Cov.: 54 AF XY: 0.851 AC XY: 618464AN XY: 726862
GnomAD4 genome ? AF: 0.748 AC: 113367AN: 151598Hom.: 45050 Cov.: 30 AF XY: 0.754 AC XY: 55862AN XY: 74060
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jun 19, 2021 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at