chr8-18208617-T-C

Variant names:

• chr8-18208617-T-C
• rs10888150
• NM_001291962.2:c.-192-1164T>C

Variant summary

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

The NM_001291962.2(NAT1):​c.-192-1164T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.477 in 152,108 control chromosomes in the GnomAD database, including 19,211 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 0.48 (19211 hom., cov: 33)
• Consequence: NAT1 NM_001291962.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.474
• Publications: 13 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=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.586 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001291962.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NAT1	NM_001291962.2		c.-192-1164T>C		intron	N/A	NP_001278891.1	F5H5R8
	NAT1	NM_001160179.3		c.-260-1164T>C		intron	N/A	NP_001153651.1	P18440

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NAT1	ENST00000903000.1		c.-378-1164T>C		intron	N/A	ENSP00000573059.1
	NAT1	ENST00000903001.1		c.-378-1164T>C		intron	N/A	ENSP00000573060.1
	NAT1	ENST00000903002.1		c.-260-1164T>C		intron	N/A	ENSP00000573061.1

Frequencies

GnomAD3 genomes AF: 0.478 AC: 72583 AN: 151990 Hom.: 19211 Cov.: 33

Gnomad AFR AF: 0.236

Gnomad AMI AF: 0.547

Gnomad AMR AF: 0.494

Gnomad ASJ AF: 0.591

Gnomad EAS AF: 0.503

Gnomad SAS AF: 0.448

Gnomad FIN AF: 0.617

Gnomad MID AF: 0.513

Gnomad NFE AF: 0.591

Gnomad OTH AF: 0.511

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

GnomAD4 genome AF: 0.477 AC: 72604 AN: 152108 Hom.: 19211 Cov.: 33 AF XY: 0.477 AC XY: 35442 AN XY: 74354

African (AFR) AF: 0.236 AC: 9803 AN: 41494

American (AMR) AF: 0.494 AC: 7560 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.591 AC: 2047 AN: 3466

East Asian (EAS) AF: 0.503 AC: 2591 AN: 5156

South Asian (SAS) AF: 0.448 AC: 2163 AN: 4824

European-Finnish (FIN) AF: 0.617 AC: 6534 AN: 10584

Middle Eastern (MID) AF: 0.503 AC: 148 AN: 294

European-Non Finnish (NFE) AF: 0.591 AC: 40183 AN: 67982

Other (OTH) AF: 0.512 AC: 1078 AN: 2106

Alfa AF: 0.550 Hom.: 67969

Bravo AF: 0.459

Asia WGS AF: 0.437 AC: 1520 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	3.4
DANN	Benign	0.49
PhyloP100		0.47
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs10888150; hg19: chr8-18066126;