XM_017012938.2:c.-7+2118A>G

Variant names:

• chr8-18389154-A-G
• rs1565684
• XM_017012938.2:c.-7+2118A>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+2118A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.469 in 152,040 control chromosomes in the GnomAD database, including 17,538 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 0.47 (17538 hom., cov: 32)
• Consequence: NAT2 XM_017012938.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.506
• Publications: 9 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=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.533 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.469 AC: 71255 AN: 151922 Hom.: 17521 Cov.: 32

Gnomad AFR AF: 0.348

Gnomad AMI AF: 0.355

Gnomad AMR AF: 0.518

Gnomad ASJ AF: 0.567

Gnomad EAS AF: 0.223

Gnomad SAS AF: 0.449

Gnomad FIN AF: 0.530

Gnomad MID AF: 0.573

Gnomad NFE AF: 0.538

Gnomad OTH AF: 0.494

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

GnomAD4 genome AF: 0.469 AC: 71317 AN: 152040 Hom.: 17538 Cov.: 32 AF XY: 0.469 AC XY: 34847 AN XY: 74310

African (AFR) AF: 0.348 AC: 14427 AN: 41456

American (AMR) AF: 0.518 AC: 7909 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.567 AC: 1968 AN: 3470

East Asian (EAS) AF: 0.223 AC: 1154 AN: 5178

South Asian (SAS) AF: 0.450 AC: 2172 AN: 4822

European-Finnish (FIN) AF: 0.530 AC: 5595 AN: 10550

Middle Eastern (MID) AF: 0.592 AC: 174 AN: 294

European-Non Finnish (NFE) AF: 0.538 AC: 36556 AN: 67978

Other (OTH) AF: 0.492 AC: 1038 AN: 2110

Alfa AF: 0.519 Hom.: 33409

Bravo AF: 0.464

Asia WGS AF: 0.339 AC: 1179 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	4.6
DANN	Benign	0.64
PhyloP100		0.51

Splicing

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

Other links and lift over

dbSNP: rs1565684; hg19: chr8-18246664;