8-18400806-G-A
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_000015.3(NAT2):c.803G>A(p.Arg268Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.592 in 1,610,782 control chromosomes in the GnomAD database, including 286,455 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 Likely benign (★). 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
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NAT2 | NM_000015.3 | c.803G>A | p.Arg268Lys | missense_variant | 2/2 | ENST00000286479.4 | |
NAT2 | XM_017012938.2 | c.803G>A | p.Arg268Lys | missense_variant | 3/3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NAT2 | ENST00000286479.4 | c.803G>A | p.Arg268Lys | missense_variant | 2/2 | 1 | NM_000015.3 | P1 | |
NAT2 | ENST00000520116.1 | c.413G>A | p.Arg138Lys | missense_variant | 2/2 | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.602 AC: 91371AN: 151750Hom.: 28047 Cov.: 31
GnomAD3 exomes AF: 0.619 AC: 153259AN: 247584Hom.: 48818 AF XY: 0.617 AC XY: 82695AN XY: 134048
GnomAD4 exome AF: 0.591 AC: 862387AN: 1458914Hom.: 258400 Cov.: 39 AF XY: 0.592 AC XY: 429292AN XY: 725744
GnomAD4 genome ? AF: 0.602 AC: 91412AN: 151868Hom.: 28055 Cov.: 31 AF XY: 0.604 AC XY: 44838AN XY: 74208
ClinVar
Submissions by phenotype
NAT2-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Nov 06, 2019 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at