dbSNP rs8190870: NAT1:c.*843C>T (chr8-18223763-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_000662.8(NAT1):c.*843C>T variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.163 in 152,228 control chromosomes in the GnomAD database, including 2,267 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 0.16 ( 2253 hom., cov: 31)

Exomes 𝑓: 0.17 ( 14 hom. )

Consequence

NAT1
NM_000662.8 downstream_gene

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.12

Variant links:

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 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-1.02).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.229 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NAT1	NM_000662.8 link	c.*843C>T		downstream_gene_variant		ENST00000307719.9	NP_000653.3	P18440

Ensembl

Gene	Transcript	HGVSc	Effect	TSL	MANE	Protein	UniProt
NAT1	ENST00000307719.9 link	c.*843C>T	downstream_gene_variant	1	NM_000662.8	ENSP00000307218.4	P18440
NAT1	ENST00000518029.5 link	c.*843C>T	downstream_gene_variant	1		ENSP00000428270.1	P18440
NAT1	ENST00000545197.3 link	c.*843C>T	downstream_gene_variant	5		ENSP00000443194.1	F5H5R8
NAT1	ENST00000517492.5 link	c.*843C>T	downstream_gene_variant	2		ENSP00000429407.1	P18440

Frequencies

GnomAD3 genomes

AF:

0.162

AC:

24590

AN:

151362

Hom.:

2246

Cov.:

show subpopulations

Gnomad AFR

AF:

0.233

Gnomad AMI

AF:

0.204

Gnomad AMR

AF:

0.0999

Gnomad ASJ

AF:

0.154

Gnomad EAS

AF:

0.0199

Gnomad SAS

AF:

0.148

Gnomad FIN

AF:

0.203

Gnomad MID

AF:

0.158

Gnomad NFE

AF:

0.140

Gnomad OTH

AF:

0.139

GnomAD4 exome

AF:

0.169

AC:

126

AN:

744

Hom.:

AF XY:

0.184

AC XY:

AN XY:

430

show subpopulations

Gnomad4 AMR exome

AF:

0.00

Gnomad4 FIN exome

AF:

0.171

Gnomad4 NFE exome

AF:

0.200

Gnomad4 OTH exome

AF:

0.00

GnomAD4 genome

AF:

0.163

AC:

24625

AN:

151484

Hom.:

2253

Cov.:

AF XY:

0.162

AC XY:

11965

AN XY:

74008

show subpopulations

Gnomad4 AFR

AF:

0.233

Gnomad4 AMR

AF:

0.0997

Gnomad4 ASJ

AF:

0.154

Gnomad4 EAS

AF:

0.0195

Gnomad4 SAS

AF:

0.149

Gnomad4 FIN

AF:

0.203

Gnomad4 NFE

AF:

0.140

Gnomad4 OTH

AF:

0.139

Alfa

AF:

0.148

Hom.:

1645

Bravo

AF:

0.158

Asia WGS

AF:

0.0990

AC:

345

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.0

CADD

Benign

0.66

DANN

Benign

0.22

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over