chr8-18371679-T-C

Variant names:

• chr8-18371679-T-C
• rs12548816

Variant summary

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

The variant allele was found at a frequency of 0.104 in 152,224 control chromosomes in the GnomAD database, including 1,009 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 0.10 (1009 hom., cov: 33)
• Consequence: NATP intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.18

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.18 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NATP		n.18371679T>C		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NATP	ENST00000523491.1	n.*195T>C		downstream_gene_variant		6

Frequencies

GnomAD3 genomes AF: 0.104 AC: 15791 AN: 152106 Hom.: 1006 Cov.: 33

Gnomad AFR AF: 0.0456

Gnomad AMI AF: 0.0592

Gnomad AMR AF: 0.186

Gnomad ASJ AF: 0.131

Gnomad EAS AF: 0.146

Gnomad SAS AF: 0.130

Gnomad FIN AF: 0.0947

Gnomad MID AF: 0.139

Gnomad NFE AF: 0.116

Gnomad OTH AF: 0.126

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.104 AC: 15808 AN: 152224 Hom.: 1009 Cov.: 33 AF XY: 0.107 AC XY: 7946 AN XY: 74450

Gnomad4 AFR AF: 0.0455

Gnomad4 AMR AF: 0.186

Gnomad4 ASJ AF: 0.131

Gnomad4 EAS AF: 0.146

Gnomad4 SAS AF: 0.131

Gnomad4 FIN AF: 0.0947

Gnomad4 NFE AF: 0.116

Gnomad4 OTH AF: 0.127

Alfa AF: 0.116 Hom.: 623

Bravo AF: 0.108

Asia WGS AF: 0.139 AC: 480 AN: 3464

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	11
DANN	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12548816; hg19: chr8-18229188;