20-2311036-C-T
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6BP7BS2
The NM_003245.4(TGM3):c.447C>T(p.His149His) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000195 in 1,614,010 control chromosomes in the GnomAD database, including 3 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
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TGM3 | NM_003245.4 | c.447C>T | p.His149His | synonymous_variant | Exon 4 of 13 | ENST00000381458.6 | NP_003236.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TGM3 | ENST00000381458.6 | c.447C>T | p.His149His | synonymous_variant | Exon 4 of 13 | 1 | NM_003245.4 | ENSP00000370867.5 | ||
ENSG00000286022 | ENST00000651531.1 | c.504C>T | p.His168His | synonymous_variant | Exon 5 of 14 | ENSP00000498584.1 |
Frequencies
GnomAD3 genomes AF: 0.000769 AC: 117AN: 152148Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000243 AC: 61AN: 251288Hom.: 0 AF XY: 0.000191 AC XY: 26AN XY: 135808
GnomAD4 exome AF: 0.000133 AC: 195AN: 1461744Hom.: 3 Cov.: 31 AF XY: 0.000133 AC XY: 97AN XY: 727188
GnomAD4 genome AF: 0.000788 AC: 120AN: 152266Hom.: 0 Cov.: 33 AF XY: 0.000806 AC XY: 60AN XY: 74444
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