rs13401811

Variant names:

• chr2-110858527-G-A
• rs13401811
• NM_001142807.4:c.788+17122G>A

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The NM_001142807.4(ACOXL):​c.788+17122G>A variant causes a intron change. The variant allele was found at a frequency of 0.188 in 152,228 control chromosomes in the GnomAD database, including 2,704 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 0.19 (2704 hom., cov: 33)
• Consequence: ACOXL NM_001142807.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.64
• Publications: 25 publications found

Genes affected

ACOXL (HGNC:25621): (acyl-CoA oxidase like) Predicted to enable acyl-CoA oxidase activity; fatty acid binding activity; and flavin adenine dinucleotide binding activity. Predicted to be involved in fatty acid beta-oxidation using acyl-CoA oxidase and lipid homeostasis. Predicted to be located in peroxisomal matrix. Predicted to be active in peroxisome. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.32).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.216 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ACOXL	NM_001142807.4	c.788+17122G>A		intron_variant	Intron 10 of 17	ENST00000439055.6	NP_001136279.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ACOXL	ENST00000439055.6	c.788+17122G>A		intron_variant	Intron 10 of 17	2	NM_001142807.4	ENSP00000407761.1

Frequencies

GnomAD3 genomes AF: 0.188 AC: 28536 AN: 152110 Hom.: 2702 Cov.: 33

Gnomad AFR AF: 0.159

Gnomad AMI AF: 0.235

Gnomad AMR AF: 0.219

Gnomad ASJ AF: 0.203

Gnomad EAS AF: 0.179

Gnomad SAS AF: 0.229

Gnomad FIN AF: 0.226

Gnomad MID AF: 0.139

Gnomad NFE AF: 0.188

Gnomad OTH AF: 0.185

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

GnomAD4 genome AF: 0.188 AC: 28548 AN: 152228 Hom.: 2704 Cov.: 33 AF XY: 0.192 AC XY: 14258 AN XY: 74430

African (AFR) AF: 0.159 AC: 6603 AN: 41526

American (AMR) AF: 0.219 AC: 3348 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.203 AC: 705 AN: 3470

East Asian (EAS) AF: 0.180 AC: 932 AN: 5192

South Asian (SAS) AF: 0.227 AC: 1097 AN: 4824

European-Finnish (FIN) AF: 0.226 AC: 2395 AN: 10610

Middle Eastern (MID) AF: 0.146 AC: 43 AN: 294

European-Non Finnish (NFE) AF: 0.188 AC: 12814 AN: 67996

Other (OTH) AF: 0.188 AC: 397 AN: 2114

Alfa AF: 0.186 Hom.: 8091

Bravo AF: 0.184

Asia WGS AF: 0.222 AC: 772 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.32
CADD	Benign	22
DANN	Benign	0.85
PhyloP100		3.6
Mutation Taster		=99/1	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs13401811; hg19: chr2-111616104;