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GeneBe

rs1208

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. 12/17 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

Genomes: 𝑓 0.60 ( 28055 hom., cov: 31)
Exomes 𝑓: 0.59 ( 258400 hom. )

Consequence

NAT2
NM_000015.3 missense

Scores

16

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.0830
Variant links:
Genes affected
NAT2 (HGNC:7646): (N-acetyltransferase 2) This gene encodes an enzyme that functions to both activate and deactivate arylamine and hydrazine drugs and carcinogens. Polymorphisms in this gene are responsible for the N-acetylation polymorphism in which human populations segregate into rapid, intermediate, and slow acetylator phenotypes. Polymorphisms in this gene are also associated with higher incidences of cancer and drug toxicity. A second polymorphic arylamine N-acetyltransferase gene (NAT1), is located near this gene (NAT2). [provided by RefSeq, Sep 2019]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4
Computational evidence support a benign effect (MetaRNN=6.8380643E-7).
BP6
Variant 8-18400806-G-A is Benign according to our data. Variant chr8-18400806-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 3059207.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.938 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
NAT2NM_000015.3 linkuse as main transcriptc.803G>A p.Arg268Lys missense_variant 2/2 ENST00000286479.4
NAT2XM_017012938.2 linkuse as main transcriptc.803G>A p.Arg268Lys missense_variant 3/3

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
NAT2ENST00000286479.4 linkuse as main transcriptc.803G>A p.Arg268Lys missense_variant 2/21 NM_000015.3 P1
NAT2ENST00000520116.1 linkuse as main transcriptc.413G>A p.Arg138Lys missense_variant 2/23

Frequencies

GnomAD3 genomes
AF:
0.602
AC:
91371
AN:
151750
Hom.:
28047
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.601
Gnomad AMI
AF:
0.677
Gnomad AMR
AF:
0.635
Gnomad ASJ
AF:
0.559
Gnomad EAS
AF:
0.960
Gnomad SAS
AF:
0.650
Gnomad FIN
AF:
0.553
Gnomad MID
AF:
0.538
Gnomad NFE
AF:
0.574
Gnomad OTH
AF:
0.594
GnomAD3 exomes
AF:
0.619
AC:
153259
AN:
247584
Hom.:
48818
AF XY:
0.617
AC XY:
82695
AN XY:
134048
show subpopulations
Gnomad AFR exome
AF:
0.597
Gnomad AMR exome
AF:
0.657
Gnomad ASJ exome
AF:
0.558
Gnomad EAS exome
AF:
0.959
Gnomad SAS exome
AF:
0.645
Gnomad FIN exome
AF:
0.558
Gnomad NFE exome
AF:
0.567
Gnomad OTH exome
AF:
0.587
GnomAD4 exome
AF:
0.591
AC:
862387
AN:
1458914
Hom.:
258400
Cov.:
39
AF XY:
0.592
AC XY:
429292
AN XY:
725744
show subpopulations
Gnomad4 AFR exome
AF:
0.595
Gnomad4 AMR exome
AF:
0.655
Gnomad4 ASJ exome
AF:
0.565
Gnomad4 EAS exome
AF:
0.965
Gnomad4 SAS exome
AF:
0.646
Gnomad4 FIN exome
AF:
0.563
Gnomad4 NFE exome
AF:
0.573
Gnomad4 OTH exome
AF:
0.600
GnomAD4 genome
AF:
0.602
AC:
91412
AN:
151868
Hom.:
28055
Cov.:
31
AF XY:
0.604
AC XY:
44838
AN XY:
74208
show subpopulations
Gnomad4 AFR
AF:
0.600
Gnomad4 AMR
AF:
0.635
Gnomad4 ASJ
AF:
0.559
Gnomad4 EAS
AF:
0.960
Gnomad4 SAS
AF:
0.649
Gnomad4 FIN
AF:
0.553
Gnomad4 NFE
AF:
0.574
Gnomad4 OTH
AF:
0.598
Alfa
AF:
0.575
Hom.:
41260
Bravo
AF:
0.607
TwinsUK
AF:
0.572
AC:
2120
ALSPAC
AF:
0.581
AC:
2238
ESP6500AA
AF:
0.601
AC:
2646
ESP6500EA
AF:
0.576
AC:
4951
ExAC
AF:
0.615
AC:
74582
Asia WGS
AF:
0.779
AC:
2709
AN:
3478
EpiCase
AF:
0.570
EpiControl
AF:
0.572

ClinVar

Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

NAT2-related condition Benign:1
Likely benign, criteria provided, single submitterclinical testingPreventionGenetics, part of Exact SciencesNov 06, 2019This 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: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.067
BayesDel_addAF
Benign
-0.84
T
BayesDel_noAF
Benign
-0.83
Cadd
Benign
1.3
Dann
Benign
0.24
Eigen
Benign
-1.3
Eigen_PC
Benign
-1.3
FATHMM_MKL
Benign
0.0028
N
LIST_S2
Benign
0.035
T;T
MetaRNN
Benign
6.8e-7
T;T
MetaSVM
Benign
-1.0
T
MutationTaster
Benign
1.0
P;P
PrimateAI
Benign
0.35
T
PROVEAN
Benign
1.4
N;N
REVEL
Benign
0.041
Sift
Benign
1.0
T;T
Sift4G
Benign
1.0
T;T
Polyphen
0.0
B;.
Vest4
0.013
MPC
0.0046
ClinPred
0.000022
T
GERP RS
1.5
gMVP
0.47

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs1208; hg19: chr8-18258316; COSMIC: COSV54061405; API