2-200613838-A-G
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_001159.4(AOX1):c.1483A>G(p.Arg495Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000682 in 1,612,428 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001159.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
AOX1 | NM_001159.4 | c.1483A>G | p.Arg495Gly | missense_variant | 15/35 | ENST00000374700.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
AOX1 | ENST00000374700.7 | c.1483A>G | p.Arg495Gly | missense_variant | 15/35 | 1 | NM_001159.4 | P1 | |
AOX1 | ENST00000485106.5 | n.392A>G | non_coding_transcript_exon_variant | 3/22 | 1 | ||||
AOX1 | ENST00000465297.5 | n.415A>G | non_coding_transcript_exon_variant | 3/23 | 2 | ||||
AOX1 | ENST00000485965.5 | n.536A>G | non_coding_transcript_exon_variant | 4/4 | 4 |
Frequencies
GnomAD3 genomes ? AF: 0.0000263 AC: 4AN: 152210Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000399 AC: 1AN: 250716Hom.: 0 AF XY: 0.00000738 AC XY: 1AN XY: 135472
GnomAD4 exome AF: 0.00000479 AC: 7AN: 1460218Hom.: 0 Cov.: 30 AF XY: 0.00000413 AC XY: 3AN XY: 726438
GnomAD4 genome ? AF: 0.0000263 AC: 4AN: 152210Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74346
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Sep 14, 2022 | The c.1483A>G (p.R495G) alteration is located in exon 15 (coding exon 15) of the AOX1 gene. This alteration results from a A to G substitution at nucleotide position 1483, causing the arginine (R) at amino acid position 495 to be replaced by a glycine (G). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at