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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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 v4.9

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;