rs1879662

chr2-73640770-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_003960.4(NAT8):c.*175T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.856 in 629,454 control chromosomes in the GnomAD database, including 231,816 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 0.87 (57239 hom., cov: 33)
  • Exomes 𝑓: 0.85 (174577 hom.)
• Consequence: NAT8 NM_003960.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.547

Genes affected

NAT8 (HGNC:18069): (N-acetyltransferase 8 (putative)) This gene, isolated using the differential display method to detect tissue-specific genes, is specifically expressed in kidney and liver. The encoded protein shows amino acid sequence similarity to N-acetyltransferases. A similar protein in Xenopus affects cell adhesion and gastrulation movements, and may be localized in the secretory pathway. A highly similar paralog is found in a cluster with this gene. [provided by RefSeq, Sep 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.904 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
NAT8	NM_003960.4	c.*175T>C		3_prime_UTR_variant	2/2	ENST00000272425.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NAT8	ENST00000272425.4	c.*175T>C		3_prime_UTR_variant	2/2	1	NM_003960.4	P1

Frequencies

GnomAD3 genomes AF: 0.866 AC: 131711 AN: 152110 Hom.: 57191 Cov.: 33

Gnomad AFR AF: 0.875

Gnomad AMI AF: 0.958

Gnomad AMR AF: 0.917

Gnomad ASJ AF: 0.816

Gnomad EAS AF: 0.679

Gnomad SAS AF: 0.823

Gnomad FIN AF: 0.851

Gnomad MID AF: 0.861

Gnomad NFE AF: 0.870

Gnomad OTH AF: 0.869

GnomAD4 exome AF: 0.853 AC: 407202 AN: 477226 Hom.: 174577 AF XY: 0.853 AC XY: 206498 AN XY: 242102

Gnomad4 AFR exome AF: 0.865

Gnomad4 AMR exome AF: 0.935

Gnomad4 ASJ exome AF: 0.824

Gnomad4 EAS exome AF: 0.670

Gnomad4 SAS exome AF: 0.830

Gnomad4 FIN exome AF: 0.849

Gnomad4 NFE exome AF: 0.869

Gnomad4 OTH exome AF: 0.861

GnomAD4 genome AF: 0.866 AC: 131818 AN: 152228 Hom.: 57239 Cov.: 33 AF XY: 0.865 AC XY: 64387 AN XY: 74436

Gnomad4 AFR AF: 0.875

Gnomad4 AMR AF: 0.917

Gnomad4 ASJ AF: 0.816

Gnomad4 EAS AF: 0.679

Gnomad4 SAS AF: 0.824

Gnomad4 FIN AF: 0.851

Gnomad4 NFE AF: 0.870

Gnomad4 OTH AF: 0.866

Alfa AF: 0.872 Hom.: 7193

Bravo AF: 0.870

Asia WGS AF: 0.776 AC: 2698 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
Cadd	Benign	3.5
Dann	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1879662; hg19: chr2-73867897;