rs13254216

Variant names:

• chr8-18371790-T-C
• rs13254216

Variant summary

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

The variant allele was found at a frequency of 0.0381 in 152,314 control chromosomes in the GnomAD database, including 155 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 0.038 (155 hom., cov: 33)
• Consequence: NATP intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.405
• Publications: 1 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=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0573 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NATP		n.18371790T>C		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0382 AC: 5809 AN: 152196 Hom.: 155 Cov.: 33

Gnomad AFR AF: 0.0104

Gnomad AMI AF: 0.0559

Gnomad AMR AF: 0.0251

Gnomad ASJ AF: 0.0280

Gnomad EAS AF: 0.000192

Gnomad SAS AF: 0.00847

Gnomad FIN AF: 0.0680

Gnomad MID AF: 0.0158

Gnomad NFE AF: 0.0588

Gnomad OTH AF: 0.0359

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

GnomAD4 genome AF: 0.0381 AC: 5808 AN: 152314 Hom.: 155 Cov.: 33 AF XY: 0.0368 AC XY: 2742 AN XY: 74484

African (AFR) AF: 0.0104 AC: 432 AN: 41574

American (AMR) AF: 0.0251 AC: 384 AN: 15306

Ashkenazi Jewish (ASJ) AF: 0.0280 AC: 97 AN: 3468

East Asian (EAS) AF: 0.000193 AC: 1 AN: 5188

South Asian (SAS) AF: 0.00848 AC: 41 AN: 4834

European-Finnish (FIN) AF: 0.0680 AC: 721 AN: 10604

Middle Eastern (MID) AF: 0.0136 AC: 4 AN: 294

European-Non Finnish (NFE) AF: 0.0588 AC: 4002 AN: 68022

Other (OTH) AF: 0.0355 AC: 75 AN: 2112

Alfa AF: 0.0490 Hom.: 34

Bravo AF: 0.0349

Asia WGS AF: 0.00696 AC: 24 AN: 3462

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	3.9
DANN	Benign	0.45
PhyloP100		-0.41

Splicing

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

Other links and lift over

dbSNP: rs13254216; hg19: chr8-18229299;