rs8190842

Variant names:

• chr8-18220936-G-A
• rs8190842
• NM_000662.8:c.-6-1106G>A

Your query was ambiguous. Multiple possible variants found:

• chr8-18220936-G-A
• chr8-18220936-G-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The NM_000662.8(NAT1):​c.-6-1106G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0259 in 152,184 control chromosomes in the GnomAD database, including 74 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 0.026 (74 hom., cov: 32)
• Consequence: NAT1 NM_000662.8 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.387
• 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=-0.91).
• BS1: Variant frequency is greater than expected in population sas. GnomAd4 allele frequency = 0.0259 (3943/152184) while in subpopulation SAS AF = 0.0367 (177/4826). AF 95% confidence interval is 0.0323. There are 74 homozygotes in GnomAd4. There are 1863 alleles in the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.
• BS2: High AC in GnomAd4 at 3943 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NAT1	NM_000662.8	c.-6-1106G>A		intron_variant	Intron 2 of 2	ENST00000307719.9	NP_000653.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NAT1	ENST00000307719.9	c.-6-1106G>A		intron_variant	Intron 2 of 2	1	NM_000662.8	ENSP00000307218.4

Frequencies

GnomAD3 genomes AF: 0.0259 AC: 3931 AN: 152066 Hom.: 74 Cov.: 32

Gnomad AFR AF: 0.0318

Gnomad AMI AF: 0.0813

Gnomad AMR AF: 0.0172

Gnomad ASJ AF: 0.0418

Gnomad EAS AF: 0.00656

Gnomad SAS AF: 0.0360

Gnomad FIN AF: 0.00878

Gnomad MID AF: 0.0791

Gnomad NFE AF: 0.0257

Gnomad OTH AF: 0.0282

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

GnomAD4 genome AF: 0.0259 AC: 3943 AN: 152184 Hom.: 74 Cov.: 32 AF XY: 0.0250 AC XY: 1863 AN XY: 74400

African (AFR) AF: 0.0318 AC: 1322 AN: 41528

American (AMR) AF: 0.0172 AC: 263 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.0418 AC: 145 AN: 3466

East Asian (EAS) AF: 0.00658 AC: 34 AN: 5168

South Asian (SAS) AF: 0.0367 AC: 177 AN: 4826

European-Finnish (FIN) AF: 0.00878 AC: 93 AN: 10590

Middle Eastern (MID) AF: 0.0850 AC: 25 AN: 294

European-Non Finnish (NFE) AF: 0.0257 AC: 1750 AN: 68008

Other (OTH) AF: 0.0284 AC: 60 AN: 2112

Alfa AF: 0.0258 Hom.: 101

Bravo AF: 0.0265

Asia WGS AF: 0.0260 AC: 91 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	4.8
DANN	Benign	0.70
PhyloP100		-0.39
Mutation Taster		=100/0	polymorphism

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs8190842; hg19: chr8-18078445;