NM_000662.8:c.*862A>T

Variant names:

• chr8-18223782-A-T
• rs8190871
• NM_000662.8:c.*862A>T

Variant summary

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

The NM_000662.8(NAT1):​c.*862A>T variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0862 in 152,162 control chromosomes in the GnomAD database, including 632 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 0.086 (628 hom., cov: 32)
  • Exomes 𝑓: 0.12 (4 hom.)
• Consequence: NAT1 NM_000662.8 downstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.58
• Publications: 1 publications found

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]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0894 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_000662.8. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NAT1	NM_000662.8	MANE Select	c.*862A>T		downstream_gene	N/A	NP_000653.3
	NAT1	NM_001160175.4		c.*862A>T		downstream_gene	N/A	NP_001153647.1
	NAT1	NM_001160176.4		c.*862A>T		downstream_gene	N/A	NP_001153648.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NAT1	ENST00000307719.9	TSL:1 MANE Select	c.*862A>T		downstream_gene	N/A	ENSP00000307218.4
	NAT1	ENST00000518029.5	TSL:1	c.*862A>T		downstream_gene	N/A	ENSP00000428270.1
	NAT1	ENST00000545197.3	TSL:5	c.*862A>T		downstream_gene	N/A	ENSP00000443194.1

Frequencies

GnomAD3 genomes AF: 0.0862 AC: 13080 AN: 151736 Hom.: 629 Cov.: 32

Gnomad AFR AF: 0.0771

Gnomad AMI AF: 0.122

Gnomad AMR AF: 0.0608

Gnomad ASJ AF: 0.104

Gnomad EAS AF: 0.0137

Gnomad SAS AF: 0.0968

Gnomad FIN AF: 0.165

Gnomad MID AF: 0.0637

Gnomad NFE AF: 0.0891

Gnomad OTH AF: 0.0776

GnomAD4 exome AF: 0.124 AC: 38 AN: 306 Hom.: 4 AF XY: 0.111 AC XY: 21 AN XY: 190

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.123 AC: 37 AN: 300

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.167 AC: 1 AN: 6

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.0861 AC: 13071 AN: 151856 Hom.: 628 Cov.: 32 AF XY: 0.0879 AC XY: 6519 AN XY: 74182

African (AFR) AF: 0.0768 AC: 3182 AN: 41406

American (AMR) AF: 0.0607 AC: 926 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.104 AC: 361 AN: 3468

East Asian (EAS) AF: 0.0133 AC: 69 AN: 5182

South Asian (SAS) AF: 0.0967 AC: 465 AN: 4810

European-Finnish (FIN) AF: 0.165 AC: 1727 AN: 10480

Middle Eastern (MID) AF: 0.0514 AC: 15 AN: 292

European-Non Finnish (NFE) AF: 0.0891 AC: 6052 AN: 67940

Other (OTH) AF: 0.0773 AC: 163 AN: 2110

Alfa AF: 0.0871 Hom.: 65

Bravo AF: 0.0776

Asia WGS AF: 0.0550 AC: 191 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	3.2
DANN	Benign	0.67
PhyloP100		1.6

Splicing

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

Other links and lift over

dbSNP: rs8190871; hg19: chr8-18081291;