rs1799931
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_000015.3(NAT2):c.857G>A(p.Gly286Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0345 in 1,592,210 control chromosomes in the GnomAD database, including 1,691 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/18 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
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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.857G>A | p.Gly286Glu | missense_variant | 2/2 | ENST00000286479.4 | |
NAT2 | XM_017012938.2 | c.857G>A | p.Gly286Glu | missense_variant | 3/3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NAT2 | ENST00000286479.4 | c.857G>A | p.Gly286Glu | missense_variant | 2/2 | 1 | NM_000015.3 | P1 | |
NAT2 | ENST00000520116.1 | c.467G>A | p.Gly156Glu | missense_variant | 2/2 | 3 |
Frequencies
GnomAD3 genomes AF: 0.0413 AC: 6284AN: 152096Hom.: 227 Cov.: 33
GnomAD3 exomes AF: 0.0576 AC: 13017AN: 226094Hom.: 682 AF XY: 0.0539 AC XY: 6612AN XY: 122612
GnomAD4 exome AF: 0.0338 AC: 48617AN: 1439998Hom.: 1463 Cov.: 32 AF XY: 0.0341 AC XY: 24432AN XY: 715712
GnomAD4 genome AF: 0.0414 AC: 6297AN: 152212Hom.: 228 Cov.: 33 AF XY: 0.0446 AC XY: 3319AN XY: 74430
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