rs8190866

Positions:

• chr8-18223693-CT-C

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2

The 8-18223693-CT-C variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.063 (390 hom., cov: 31)
  • Exomes 𝑓: 0.098 (22 hom.)
  • Failed GnomAD Quality Control
• Consequence: NAT1 NM_000662.8 downstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.717

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 Likely_benign. Variant got -4 ACMG points.

• BS2: High AC in GnomAdExome4 at 883 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
NAT1	NM_000662.8			downstream_gene_variant		ENST00000307719.9	NP_000653.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
NAT1	ENST00000307719.9			downstream_gene_variant		1	NM_000662.8	ENSP00000307218	P1
NAT1	ENST00000518029.5			downstream_gene_variant		1		ENSP00000428270	P1
NAT1	ENST00000517492.5			downstream_gene_variant		2		ENSP00000429407	P1
NAT1	ENST00000545197.3			downstream_gene_variant		5		ENSP00000443194

Frequencies

GnomAD3 genomes AF: 0.00 AC: 9559 AN: 150336 Hom.: 392 Cov.: 31 FAILED QC

Gnomad AFR AF: 0.0201

Gnomad AMI AF: 0.120

Gnomad AMR AF: 0.0508

Gnomad ASJ AF: 0.0950

Gnomad EAS AF: 0.0122

Gnomad SAS AF: 0.0938

Gnomad FIN AF: 0.136

Gnomad MID AF: 0.0570

Gnomad NFE AF: 0.0820

Gnomad OTH AF: 0.0572

GnomAD4 exome AF: 0.0975 AC: 883 AN: 9052 Hom.: 22 Cov.: 0 AF XY: 0.101 AC XY: 444 AN XY: 4412

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 FIN exome AF: 0.0987

Gnomad4 NFE exome AF: 0.0143

Gnomad4 OTH exome AF: 0.0370

GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.0635 AC: 9550 AN: 150454 Hom.: 390 Cov.: 31 AF XY: 0.0649 AC XY: 4758 AN XY: 73348

Gnomad4 AFR AF: 0.0200

Gnomad4 AMR AF: 0.0507

Gnomad4 ASJ AF: 0.0950

Gnomad4 EAS AF: 0.0118

Gnomad4 SAS AF: 0.0933

Gnomad4 FIN AF: 0.136

Gnomad4 NFE AF: 0.0820

Gnomad4 OTH AF: 0.0570

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs8190866; hg19: chr8-18081202;