rs4345600

Variant names:

• chr8-18390698-A-G
• rs4345600
• XM_017012938.2:c.-7+3662A>G

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+3662A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.108 in 149,752 control chromosomes in the GnomAD database, including 1,052 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 0.11 (1052 hom., cov: 32)
• Consequence: NAT2 XM_017012938.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.366
• Publications: 11 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=-0.83).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.178 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NAT2	XM_017012938.2	c.-7+3662A>G		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: 0.108 AC: 16175 AN: 149644 Hom.: 1048 Cov.: 32

Gnomad AFR AF: 0.0439

Gnomad AMI AF: 0.0586

Gnomad AMR AF: 0.183

Gnomad ASJ AF: 0.146

Gnomad EAS AF: 0.180

Gnomad SAS AF: 0.159

Gnomad FIN AF: 0.102

Gnomad MID AF: 0.155

Gnomad NFE AF: 0.120

Gnomad OTH AF: 0.129

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

GnomAD4 genome AF: 0.108 AC: 16190 AN: 149752 Hom.: 1052 Cov.: 32 AF XY: 0.111 AC XY: 8145 AN XY: 73088

African (AFR) AF: 0.0438 AC: 1796 AN: 40980

American (AMR) AF: 0.183 AC: 2738 AN: 14924

Ashkenazi Jewish (ASJ) AF: 0.146 AC: 503 AN: 3438

East Asian (EAS) AF: 0.180 AC: 927 AN: 5140

South Asian (SAS) AF: 0.160 AC: 750 AN: 4702

European-Finnish (FIN) AF: 0.102 AC: 1028 AN: 10092

Middle Eastern (MID) AF: 0.167 AC: 48 AN: 288

European-Non Finnish (NFE) AF: 0.120 AC: 8075 AN: 67214

Other (OTH) AF: 0.131 AC: 272 AN: 2070

Alfa AF: 0.120 Hom.: 1179

Bravo AF: 0.110

Asia WGS AF: 0.153 AC: 531 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	2.1
DANN	Benign	0.89
PhyloP100		-0.37

Splicing

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

Other links and lift over

dbSNP: rs4345600; hg19: chr8-18248208;