ENST00000523491.1:n.1A>G

Variant names:

• chr8-18370607-A-G
• rs10088180
• ENST00000523491.1:n.1A>G

Variant summary

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

The ENST00000523491.1(NATP):​n.1A>G variant causes a non coding transcript exon change. The variant allele was found at a frequency of 0.649 in 153,810 control chromosomes in the GnomAD database, including 33,032 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 0.65 (33002 hom., cov: 32)
  • Exomes 𝑓: 0.15 (30 hom.)
• Consequence: NATP ENST00000523491.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 6.53
• Publications: 5 publications found

Genes affected

NATP (HGNC:15): (N-acetyltransferase pseudogene)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.59).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.698 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000523491.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NATP	ENST00000523491.1	TSL:6	n.1A>G		non_coding_transcript_exon	Exon 1 of 1

Frequencies

GnomAD3 genomes AF: 0.654 AC: 99457 AN: 151962 Hom.: 32992 Cov.: 32

Gnomad AFR AF: 0.650

Gnomad AMI AF: 0.813

Gnomad AMR AF: 0.533

Gnomad ASJ AF: 0.684

Gnomad EAS AF: 0.348

Gnomad SAS AF: 0.661

Gnomad FIN AF: 0.656

Gnomad MID AF: 0.677

Gnomad NFE AF: 0.703

Gnomad OTH AF: 0.651

GnomAD4 exome AF: 0.147 AC: 254 AN: 1730 Hom.: 30 Cov.: 0 AF XY: 0.178 AC XY: 174 AN XY: 980

⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.

African (AFR) AF: 0.125 AC: 5 AN: 40

American (AMR) AF: 0.0603 AC: 21 AN: 348

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 12

East Asian (EAS) AF: 0.0116 AC: 3 AN: 258

South Asian (SAS) AF: 0.0932 AC: 11 AN: 118

European-Finnish (FIN) AF: 0.199 AC: 37 AN: 186

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.219 AC: 153 AN: 698

Other (OTH) AF: 0.343 AC: 24 AN: 70

⚠️ The allele balance in gnomAD4 Exomes is highly skewed from 0.5 (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.

GnomAD4 genome AF: 0.654 AC: 99508 AN: 152080 Hom.: 33002 Cov.: 32 AF XY: 0.646 AC XY: 48006 AN XY: 74344

African (AFR) AF: 0.650 AC: 26931 AN: 41450

American (AMR) AF: 0.533 AC: 8141 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.684 AC: 2375 AN: 3470

East Asian (EAS) AF: 0.349 AC: 1806 AN: 5174

South Asian (SAS) AF: 0.661 AC: 3189 AN: 4826

European-Finnish (FIN) AF: 0.656 AC: 6927 AN: 10566

Middle Eastern (MID) AF: 0.680 AC: 200 AN: 294

European-Non Finnish (NFE) AF: 0.703 AC: 47833 AN: 68004

Other (OTH) AF: 0.646 AC: 1365 AN: 2112

Alfa AF: 0.682 Hom.: 28629

Bravo AF: 0.641

Asia WGS AF: 0.502 AC: 1746 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.59
CADD	Benign	13
DANN	Benign	0.59
PhyloP100		6.5

Splicing

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

Other links and lift over

dbSNP: rs10088180; hg19: chr8-18228116;