3-101565275-T-A
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_017819.4(TRMT10C):c.494T>A(p.Leu165Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00037 in 1,612,164 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_017819.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TRMT10C | NM_017819.4 | c.494T>A | p.Leu165Gln | missense_variant | 2/2 | ENST00000309922.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TRMT10C | ENST00000309922.7 | c.494T>A | p.Leu165Gln | missense_variant | 2/2 | 1 | NM_017819.4 | P1 | |
TRMT10C | ENST00000495642.1 | c.494T>A | p.Leu165Gln | missense_variant | 2/2 | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.00207 AC: 315AN: 152148Hom.: 1 Cov.: 32
GnomAD3 exomes AF: 0.000536 AC: 133AN: 247964Hom.: 1 AF XY: 0.000438 AC XY: 59AN XY: 134732
GnomAD4 exome AF: 0.000193 AC: 282AN: 1459898Hom.: 0 Cov.: 33 AF XY: 0.000156 AC XY: 113AN XY: 726132
GnomAD4 genome ? AF: 0.00207 AC: 315AN: 152266Hom.: 1 Cov.: 32 AF XY: 0.00203 AC XY: 151AN XY: 74452
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Nov 11, 2022 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at