rs7388368

Positions:

• chr8-18197877-A-C
• chr8-18197877-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001291962.2(NAT1):​c.-192-11904A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.792 in 151,262 control chromosomes in the GnomAD database, including 47,760 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 0.79 (47760 hom., cov: 28)
• Consequence: NAT1 NM_001291962.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.639

Genes affected

NAT1 (HGNC:7645): (N-acetyltransferase 1) This gene is one of two arylamine N-acetyltransferase (NAT) genes in the human genome, and is orthologous to the mouse and rat Nat2 genes. The enzyme encoded by this gene catalyzes the transfer of an acetyl group from acetyl-CoA to various arylamine and hydrazine substrates. This enzyme helps metabolize drugs and other xenobiotics, and functions in folate catabolism. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Aug 2011]

NAT1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.866 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
NAT1	NM_001291962.2	c.-192-11904A>C		intron_variant			NP_001278891.1
NAT1	NM_001160179.3	c.-260-11904A>C		intron_variant			NP_001153651.1
NAT1	XM_047422397.1	c.-815-11904A>C		intron_variant			XP_047278353.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
NAT1	ENST00000517441.5	n.93-11904A>C		intron_variant		2

Frequencies

GnomAD3 genomes AF: 0.792 AC: 119664 AN: 151160 Hom.: 47728 Cov.: 28

Gnomad AFR AF: 0.875

Gnomad AMI AF: 0.764

Gnomad AMR AF: 0.743

Gnomad ASJ AF: 0.781

Gnomad EAS AF: 0.595

Gnomad SAS AF: 0.670

Gnomad FIN AF: 0.766

Gnomad MID AF: 0.869

Gnomad NFE AF: 0.780

Gnomad OTH AF: 0.799

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

GnomAD4 genome AF: 0.792 AC: 119739 AN: 151262 Hom.: 47760 Cov.: 28 AF XY: 0.786 AC XY: 58009 AN XY: 73842

Gnomad4 AFR AF: 0.874

Gnomad4 AMR AF: 0.744

Gnomad4 ASJ AF: 0.781

Gnomad4 EAS AF: 0.594

Gnomad4 SAS AF: 0.670

Gnomad4 FIN AF: 0.766

Gnomad4 NFE AF: 0.780

Gnomad4 OTH AF: 0.797

Alfa AF: 0.772 Hom.: 7219

Bravo AF: 0.795

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	4.1
DANN	Benign	0.43

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7388368; hg19: chr8-18055386; COSMIC: COSV72832002;