16-58708286-C-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_002080.4(GOT2):c.1178G>A(p.Arg393Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000188 in 1,613,794 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R393W) has been classified as Likely benign.
Frequency
Consequence
NM_002080.4 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 |
---|---|---|---|---|---|---|---|
GOT2 | NM_002080.4 | c.1178G>A | p.Arg393Gln | missense_variant | 10/10 | ENST00000245206.10 | |
GOT2 | NM_001286220.2 | c.1049G>A | p.Arg350Gln | missense_variant | 9/9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GOT2 | ENST00000245206.10 | c.1178G>A | p.Arg393Gln | missense_variant | 10/10 | 1 | NM_002080.4 | P1 | |
GOT2 | ENST00000434819.2 | c.1049G>A | p.Arg350Gln | missense_variant | 9/9 | 2 |
Frequencies
GnomAD3 genomes AF: 0.000808 AC: 123AN: 152180Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000207 AC: 52AN: 250608Hom.: 0 AF XY: 0.000125 AC XY: 17AN XY: 135488
GnomAD4 exome AF: 0.000122 AC: 179AN: 1461496Hom.: 0 Cov.: 30 AF XY: 0.000103 AC XY: 75AN XY: 727064
GnomAD4 genome AF: 0.000814 AC: 124AN: 152298Hom.: 0 Cov.: 33 AF XY: 0.000819 AC XY: 61AN XY: 74470
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Oct 03, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at