rs1731017
Variant summary
Our verdict is Benign. The variant received -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_020686.6(ABAT):c.167A>G(p.Gln56Arg) variant causes a missense, splice region change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.604 in 1,611,140 control chromosomes in the GnomAD database, including 297,905 homozygotes. In-silico tool predicts a benign outcome for this variant. 17/23 in silico tools predict a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Benign (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. Q56L) has been classified as Uncertain significance.
Frequency
Consequence
NM_020686.6 missense, splice_region
Scores
Clinical Significance
Conservation
Publications
- GABA aminotransaminase deficiencyInheritance: AR Classification: DEFINITIVE, STRONG, MODERATE, SUPPORTIVE Submitted by: Ambry Genetics, G2P, Labcorp Genetics (formerly Invitae), Orphanet
- genetic developmental and epileptic encephalopathyInheritance: AR Classification: MODERATE Submitted by: ClinGen
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ACMG classification
Our verdict: Benign. The variant received -20 ACMG points.
Variant Effect in Transcripts
ACMG analysis was done for transcript: NM_020686.6. You can select a different transcript below to see updated ACMG assignments.
RefSeq Transcripts
| Sel. | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| ABAT | MANE Select | c.167A>G | p.Gln56Arg | missense splice_region | Exon 3 of 16 | NP_065737.2 | |||
| ABAT | c.167A>G | p.Gln56Arg | missense splice_region | Exon 3 of 17 | NP_001373544.1 | ||||
| ABAT | c.167A>G | p.Gln56Arg | missense splice_region | Exon 3 of 16 | NP_001373545.1 | H3BNQ7 |
Ensembl Transcripts
| Sel. | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| ABAT | TSL:1 MANE Select | c.167A>G | p.Gln56Arg | missense splice_region | Exon 3 of 16 | ENSP00000268251.8 | P80404 | ||
| ABAT | TSL:1 | c.167A>G | p.Gln56Arg | missense splice_region | Exon 3 of 16 | ENSP00000454963.1 | H3BNQ7 | ||
| ABAT | TSL:1 | n.71-2011A>G | intron | N/A | ENSP00000455198.1 | H3BP84 |
Frequencies
GnomAD3 genomes AF: 0.534 AC: 81051AN: 151816Hom.: 22937 Cov.: 31 show subpopulations
GnomAD2 exomes AF: 0.591 AC: 148349AN: 250938 AF XY: 0.589 show subpopulations
GnomAD4 exome AF: 0.611 AC: 891448AN: 1459204Hom.: 274957 Cov.: 35 AF XY: 0.608 AC XY: 441590AN XY: 725956 show subpopulations
Age Distribution
GnomAD4 genome AF: 0.534 AC: 81089AN: 151936Hom.: 22948 Cov.: 31 AF XY: 0.534 AC XY: 39649AN XY: 74250 show subpopulations
Age Distribution
ClinVar
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at