rs1799930
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_000015.3(NAT2):c.590G>A(p.Arg197Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.273 in 151716 control chromosomes in the gnomAD Genomes database, including 5835 homozygotes. In-silico tool predicts a benign outcome for this variant. 10/17 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as drug response (no stars). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_000015.3 missense
Scores
Clinical Significance
Conservation
Links
ACMG classification
Verdict is Benign. Variant got -12 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NAT2 | NM_000015.3 | c.590G>A | p.Arg197Gln | missense_variant | 2/2 | ENST00000286479.4 | |
NAT2 | XM_017012938.2 | c.590G>A | p.Arg197Gln | missense_variant | 3/3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NAT2 | ENST00000286479.4 | c.590G>A | p.Arg197Gln | missense_variant | 2/2 | 1 | NM_000015.3 | P1 | |
NAT2 | ENST00000520116.1 | c.200G>A | p.Arg67Gln | missense_variant | 2/2 | 3 |
Frequencies
GnomAD3 genomes AF: 0.273 AC: 41457AN: 151716Hom.: 5835 Cov.: 31
GnomAD3 exomes AF: 0.273 AC: 68188AN: 249910Hom.: 9856 AF XY: 0.282 AC XY: 38067AN XY: 135124
GnomAD4 exome AF: 0.289 AC: 422623AN: 1460740Hom.: 62400 AF XY: 0.292 AC XY: 212083AN XY: 726624
ClinVar
Submissions by phenotype
Slow acetylator due to N-acetyltransferase enzyme variant Other:1
drug response, no assertion criteria provided | literature only | OMIM | Oct 28, 2012 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at