chr20-2311076-A-C
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_003245.4(TGM3):c.487A>C(p.Ile163Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0198 in 1,614,048 control chromosomes in the GnomAD database, including 5,324 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_003245.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TGM3 | NM_003245.4 | c.487A>C | p.Ile163Leu | missense_variant | 4/13 | ENST00000381458.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TGM3 | ENST00000381458.6 | c.487A>C | p.Ile163Leu | missense_variant | 4/13 | 1 | NM_003245.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.105 AC: 15925AN: 152090Hom.: 2823 Cov.: 32
GnomAD3 exomes AF: 0.0272 AC: 6831AN: 251408Hom.: 1086 AF XY: 0.0194 AC XY: 2638AN XY: 135874
GnomAD4 exome AF: 0.0109 AC: 15931AN: 1461840Hom.: 2495 Cov.: 31 AF XY: 0.00943 AC XY: 6858AN XY: 727218
GnomAD4 genome ? AF: 0.105 AC: 15960AN: 152208Hom.: 2829 Cov.: 32 AF XY: 0.100 AC XY: 7473AN XY: 74450
ClinVar
Submissions by phenotype
TGM3-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Nov 25, 2019 | This variant is classified as 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