rs28359534

chr8-18223324-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The NM_000662.8(NAT1):c.*404A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0173 in 167,176 control chromosomes in the GnomAD database, including 50 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 0.018 (49 hom., cov: 32)
  • Exomes 𝑓: 0.0087 (1 hom.)
• Consequence: NAT1 NM_000662.8 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.579

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BS1: Variant frequency is greater than expected in population sas. gnomad4 allele frequency = 0.0182 (2764/152286) while in subpopulation SAS AF= 0.0364 (176/4832). AF 95% confidence interval is 0.032. There are 49 homozygotes in gnomad4. There are 1299 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
• BS2: High AC in GnomAd at 2756 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
NAT1	NM_000662.8	c.*404A>G		3_prime_UTR_variant	3/3	ENST00000307719.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NAT1	ENST00000307719.9	c.*404A>G		3_prime_UTR_variant	3/3	1	NM_000662.8	P1
NAT1	ENST00000518029.5	c.*404A>G		3_prime_UTR_variant	4/4	1		P1
NAT1	ENST00000517492.5	c.*404A>G		3_prime_UTR_variant	3/3	2		P1
NAT1	ENST00000545197.3	c.*404A>G		3_prime_UTR_variant	4/4	5

Frequencies

GnomAD3 genomes AF: 0.0181 AC: 2756 AN: 152168 Hom.: 49 Cov.: 32

Gnomad AFR AF: 0.00487

Gnomad AMI AF: 0.0811

Gnomad AMR AF: 0.0147

Gnomad ASJ AF: 0.0421

Gnomad EAS AF: 0.00653

Gnomad SAS AF: 0.0358

Gnomad FIN AF: 0.00878

Gnomad MID AF: 0.0791

Gnomad NFE AF: 0.0255

Gnomad OTH AF: 0.0229

GnomAD4 exome AF: 0.00866 AC: 129 AN: 14890 Hom.: 1 Cov.: 0 AF XY: 0.0103 AC XY: 73 AN XY: 7084

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00824

Gnomad4 NFE exome AF: 0.0714

Gnomad4 OTH exome AF: 0.0111

GnomAD4 genome AF: 0.0182 AC: 2764 AN: 152286 Hom.: 49 Cov.: 32 AF XY: 0.0174 AC XY: 1299 AN XY: 74472

Gnomad4 AFR AF: 0.00491

Gnomad4 AMR AF: 0.0147

Gnomad4 ASJ AF: 0.0421

Gnomad4 EAS AF: 0.00655

Gnomad4 SAS AF: 0.0364

Gnomad4 FIN AF: 0.00878

Gnomad4 NFE AF: 0.0256

Gnomad4 OTH AF: 0.0232

Alfa AF: 0.0217 Hom.: 9

Bravo AF: 0.0174

Asia WGS AF: 0.0240 AC: 83 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	0.99
Dann	Benign	0.40

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

Publications

LitVar

Other links and lift over

dbSNP: rs28359534; hg19: chr8-18080833;