rs4271002

Variant names:

• chr8-18390758-G-C
• rs4271002
• XM_017012938.2:c.-7+3722G>C

Your query was ambiguous. Multiple possible variants found:

• chr8-18390758-G-C
• chr8-18390758-G-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XM_017012938.2(NAT2):​c.-7+3722G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.117 in 152,064 control chromosomes in the GnomAD database, including 1,152 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.12 (1152 hom., cov: 32)
• Consequence: NAT2 XM_017012938.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.17
• Publications: 25 publications found

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]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.177 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NAT2	XM_017012938.2	c.-7+3722G>C		intron_variant	Intron 2 of 2		XP_016868427.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.117 AC: 17791 AN: 151944 Hom.: 1148 Cov.: 32

Gnomad AFR AF: 0.0799

Gnomad AMI AF: 0.0581

Gnomad AMR AF: 0.183

Gnomad ASJ AF: 0.145

Gnomad EAS AF: 0.180

Gnomad SAS AF: 0.156

Gnomad FIN AF: 0.0977

Gnomad MID AF: 0.155

Gnomad NFE AF: 0.119

Gnomad OTH AF: 0.135

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.117 AC: 17811 AN: 152064 Hom.: 1152 Cov.: 32 AF XY: 0.121 AC XY: 8956 AN XY: 74316

African (AFR) AF: 0.0798 AC: 3311 AN: 41496

American (AMR) AF: 0.183 AC: 2795 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.145 AC: 501 AN: 3462

East Asian (EAS) AF: 0.180 AC: 926 AN: 5144

South Asian (SAS) AF: 0.157 AC: 754 AN: 4816

European-Finnish (FIN) AF: 0.0977 AC: 1032 AN: 10562

Middle Eastern (MID) AF: 0.167 AC: 49 AN: 294

European-Non Finnish (NFE) AF: 0.119 AC: 8101 AN: 67986

Other (OTH) AF: 0.137 AC: 289 AN: 2110

Alfa AF: 0.119 Hom.: 175

Bravo AF: 0.122

Asia WGS AF: 0.156 AC: 540 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.24
DANN	Benign	0.45
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs4271002; hg19: chr8-18248268;