rs3812475
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_017956.4(TRMT12):āc.82T>Cā(p.Trp28Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.496 in 1,613,798 control chromosomes in the GnomAD database, including 201,862 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. 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. W28S) has been classified as Uncertain significance.
Frequency
Consequence
NM_017956.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -12 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TRMT12 | NM_017956.4 | c.82T>C | p.Trp28Arg | missense_variant | 1/1 | ENST00000328599.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TRMT12 | ENST00000328599.4 | c.82T>C | p.Trp28Arg | missense_variant | 1/1 | NM_017956.4 | P1 | ||
TRMT12 | ENST00000521443.1 | n.190T>C | non_coding_transcript_exon_variant | 1/2 | 4 | ||||
TRMT12 | ENST00000522518.1 | c.82T>C | p.Trp28Arg | missense_variant, NMD_transcript_variant | 1/3 | 3 |
Frequencies
GnomAD3 genomes AF: 0.548 AC: 83225AN: 151880Hom.: 23790 Cov.: 31
GnomAD3 exomes AF: 0.503 AC: 126448AN: 251402Hom.: 32511 AF XY: 0.502 AC XY: 68250AN XY: 135872
GnomAD4 exome AF: 0.491 AC: 717387AN: 1461798Hom.: 178024 Cov.: 51 AF XY: 0.491 AC XY: 357381AN XY: 727206
GnomAD4 genome AF: 0.548 AC: 83316AN: 152000Hom.: 23838 Cov.: 31 AF XY: 0.548 AC XY: 40718AN XY: 74278
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at