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GeneBe

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

Genomes: 𝑓 0.27 ( 5835 hom., cov: 31)
Exomes 𝑓: 0.27 ( 9856 hom. )

Consequence

NAT2
NM_000015.3 missense

Scores

1
1
14

Clinical Significance

drug response no assertion criteria provided O:1

Conservation

PhyloP100: 1.09

Links

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
?
Computational evidence support a benign effect (MetaRNN=4.61936E-4).
BA1
?
GnomAd highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.352 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
NAT2NM_000015.3 linkuse as main transcriptc.590G>A p.Arg197Gln missense_variant 2/2 ENST00000286479.4
NAT2XM_017012938.2 linkuse as main transcriptc.590G>A p.Arg197Gln missense_variant 3/3

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
NAT2ENST00000286479.4 linkuse as main transcriptc.590G>A p.Arg197Gln missense_variant 2/21 NM_000015.3 P1
NAT2ENST00000520116.1 linkuse as main transcriptc.200G>A p.Arg67Gln missense_variant 2/23

Frequencies

GnomAD3 genomes
AF:
0.273
AC:
41457
AN:
151716
Hom.:
5835
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.259
Gnomad AMI
AF:
0.353
Gnomad AMR
AF:
0.207
Gnomad ASJ
AF:
0.362
Gnomad EAS
AF:
0.256
Gnomad SAS
AF:
0.366
Gnomad FIN
AF:
0.234
Gnomad MID
AF:
0.287
Gnomad NFE
AF:
0.292
Gnomad OTH
AF:
0.274
GnomAD3 exomes
AF:
0.273
AC:
68188
AN:
249910
Hom.:
9856
AF XY:
0.282
AC XY:
38067
AN XY:
135124
show subpopulations
Gnomad AFR exome
AF:
0.257
Gnomad AMR exome
AF:
0.156
Gnomad ASJ exome
AF:
0.354
Gnomad EAS exome
AF:
0.258
Gnomad SAS exome
AF:
0.362
Gnomad FIN exome
AF:
0.237
Gnomad NFE exome
AF:
0.289
Gnomad OTH exome
AF:
0.276
GnomAD4 exome
AF:
0.289
AC:
422623
AN:
1460740
Hom.:
62400
AF XY:
0.292
AC XY:
212083
AN XY:
726624
show subpopulations
Gnomad4 AFR exome
AF:
0.257
Gnomad4 AMR exome
AF:
0.160
Gnomad4 ASJ exome
AF:
0.364
Gnomad4 EAS exome
AF:
0.222
Gnomad4 SAS exome
AF:
0.359
Gnomad4 FIN exome
AF:
0.240
Gnomad4 NFE exome
AF:
0.293
Gnomad4 OTH exome
AF:
0.296
Alfa
AF:
0.283
Hom.:
15609
Bravo
AF:
0.264
TwinsUK
AF:
0.290
AC:
1076
ALSPAC
AF:
0.303
AC:
1168
ESP6500AA
AF:
0.266
AC:
1171
ESP6500EA
AF:
0.290
AC:
2497
ExAC
AF:
0.277
AC:
33610
Asia WGS
AF:
0.314
AC:
1091
AN:
3478
EpiCase
AF:
0.294
EpiControl
AF:
0.294

ClinVar

Significance: drug response
Submissions summary: Other:1
Revision: no assertion criteria provided
LINK: link

Submissions by phenotype

Slow acetylator due to N-acetyltransferase enzyme variant Other:1
drug response, no assertion criteria providedliterature onlyOMIMOct 28, 2012- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.10
BayesDel_addAF
Benign
-0.55
T
BayesDel_noAF
Benign
-0.42
Cadd
Benign
22
Dann
Pathogenic
1.0
Eigen
Benign
0.088
Eigen_PC
Benign
-0.13
FATHMM_MKL
Benign
0.38
N
LIST_S2
Benign
0.83
T;T
MetaRNN
Benign
0.00046
T;T
MetaSVM
Benign
-0.94
T
MutationTaster
Benign
0.0016
P;P
PrimateAI
Benign
0.24
T
PROVEAN
Uncertain
-2.8
D;D
REVEL
Benign
0.17
Sift
Benign
0.054
T;T
Sift4G
Benign
0.091
T;D
Polyphen
1.0
D;.
Vest4
0.082
MPC
0.0095
ClinPred
0.042
T
GERP RS
2.5
gMVP
0.69

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: rs1799930; hg19: chr8-18258103; COSMIC: COSV54061522;