1-100140185-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_019083.3(TRMT13):c.328C>T(p.Pro110Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000106 in 1,606,284 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar 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 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TRMT13 | NM_019083.3 | c.328C>T | p.Pro110Ser | missense_variant | 5/11 | ENST00000370141.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TRMT13 | ENST00000370141.8 | c.328C>T | p.Pro110Ser | missense_variant | 5/11 | 1 | NM_019083.3 | P1 | |
TRMT13 | ENST00000370139.1 | c.235C>T | p.Pro79Ser | missense_variant | 5/6 | 3 | |||
TRMT13 | ENST00000370143.5 | c.325-223C>T | intron_variant | 3 | |||||
TRMT13 | ENST00000482437.5 | c.328C>T | p.Pro110Ser | missense_variant, NMD_transcript_variant | 5/8 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.00000658 AC: 1AN: 152044Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.00000409 AC: 1AN: 244728Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 132598
GnomAD4 exome AF: 0.0000110 AC: 16AN: 1454240Hom.: 0 Cov.: 30 AF XY: 0.00000553 AC XY: 4AN XY: 723510
GnomAD4 genome ? AF: 0.00000658 AC: 1AN: 152044Hom.: 0 Cov.: 33 AF XY: 0.0000135 AC XY: 1AN XY: 74236
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 14, 2023 | The c.328C>T (p.P110S) alteration is located in exon 5 (coding exon 5) of the TRMT13 gene. This alteration results from a C to T substitution at nucleotide position 328, causing the proline (P) at amino acid position 110 to be replaced by a serine (S). 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