20-2309727-C-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6BP7
The NM_003245.4(TGM3):c.78C>T(p.Ser26Ser) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000235 in 1,614,192 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (no stars).
Frequency
Consequence
NM_003245.4 synonymous
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TGM3 | NM_003245.4 | c.78C>T | p.Ser26Ser | synonymous_variant | Exon 2 of 13 | ENST00000381458.6 | NP_003236.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TGM3 | ENST00000381458.6 | c.78C>T | p.Ser26Ser | synonymous_variant | Exon 2 of 13 | 1 | NM_003245.4 | ENSP00000370867.5 | ||
ENSG00000286022 | ENST00000651531.1 | c.135C>T | p.Ser45Ser | synonymous_variant | Exon 3 of 14 | ENSP00000498584.1 |
Frequencies
GnomAD3 genomes AF: 0.00109 AC: 166AN: 152194Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000362 AC: 91AN: 251340Hom.: 0 AF XY: 0.000243 AC XY: 33AN XY: 135832
GnomAD4 exome AF: 0.000146 AC: 213AN: 1461880Hom.: 1 Cov.: 38 AF XY: 0.000124 AC XY: 90AN XY: 727246
GnomAD4 genome AF: 0.00110 AC: 167AN: 152312Hom.: 0 Cov.: 33 AF XY: 0.00111 AC XY: 83AN XY: 74468
ClinVar
Submissions by phenotype
TGM3-related disorder Benign:1
This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at