Variant rs1799930 details in Genebe, Genetics Data Aggregator

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

Clinical Significance

drug response no assertion criteria provided O:1

Conservation

PhyloP100: 1.09

Links

NAT2 (HGNC:7646):

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
NAT2	NM_000015.3 linkuse as main transcript	c.590G>A	p.Arg197Gln	missense_variant	2/2	ENST00000286479.4
NAT2	XM_017012938.2 linkuse as main transcript	c.590G>A	p.Arg197Gln	missense_variant	3/3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NAT2	ENST00000286479.4 linkuse as main transcript	c.590G>A	p.Arg197Gln	missense_variant	2/2	1	NM_000015.3	P1
NAT2	ENST00000520116.1 linkuse as main transcript	c.200G>A	p.Arg67Gln	missense_variant	2/2	3

Frequencies

GnomAD3 genomes

AF:

0.273

AC:

41457

AN:

151716

Hom.:

5835

Cov.:

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 provided

literature only

OMIM

Oct 28, 2012

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.10

BayesDel_addAF

Benign

-0.55

BayesDel_noAF

Benign

-0.42

Cadd

Benign

Dann

Pathogenic

1.0

Eigen

Benign

0.088

Eigen_PC

Benign

-0.13

FATHMM_MKL

Benign

0.38

LIST_S2

Benign

0.83

T;T

MetaRNN

Benign

0.00046

T;T

MetaSVM

Benign

-0.94

MutationTaster

Benign

0.0016

P;P

PrimateAI

Benign

0.24

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

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Links

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over