rs17483466

Variant names:

• chr2-111039881-A-G
• rs17483466
• NM_001142807.4:c.1369+8167A>G

Variant summary

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

The NM_001142807.4(ACOXL):​c.1369+8167A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.152 in 152,262 control chromosomes in the GnomAD database, including 2,150 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 0.15 (2150 hom., cov: 33)
• Consequence: ACOXL NM_001142807.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.391
• Publications: 53 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]

MIR4435-2HG (HGNC:35163): (MIR4435-2 host gene)

LOC124907866 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.199 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ACOXL	NM_001142807.4	c.1369+8167A>G		intron_variant	Intron 15 of 17	ENST00000439055.6	NP_001136279.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ACOXL	ENST00000439055.6	c.1369+8167A>G		intron_variant	Intron 15 of 17	2	NM_001142807.4	ENSP00000407761.1

Frequencies

GnomAD3 genomes AF: 0.153 AC: 23207 AN: 152144 Hom.: 2147 Cov.: 33

Gnomad AFR AF: 0.0660

Gnomad AMI AF: 0.226

Gnomad AMR AF: 0.191

Gnomad ASJ AF: 0.232

Gnomad EAS AF: 0.0106

Gnomad SAS AF: 0.139

Gnomad FIN AF: 0.157

Gnomad MID AF: 0.225

Gnomad NFE AF: 0.201

Gnomad OTH AF: 0.185

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

GnomAD4 genome AF: 0.152 AC: 23214 AN: 152262 Hom.: 2150 Cov.: 33 AF XY: 0.152 AC XY: 11291 AN XY: 74438

African (AFR) AF: 0.0660 AC: 2743 AN: 41570

American (AMR) AF: 0.191 AC: 2916 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.232 AC: 804 AN: 3470

East Asian (EAS) AF: 0.0108 AC: 56 AN: 5190

South Asian (SAS) AF: 0.140 AC: 675 AN: 4828

European-Finnish (FIN) AF: 0.157 AC: 1666 AN: 10588

Middle Eastern (MID) AF: 0.221 AC: 65 AN: 294

European-Non Finnish (NFE) AF: 0.201 AC: 13696 AN: 68006

Other (OTH) AF: 0.183 AC: 387 AN: 2114

Alfa AF: 0.189 Hom.: 14153

Bravo AF: 0.151

Asia WGS AF: 0.0820 AC: 285 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	2.5
DANN	Benign	0.56
PhyloP100		-0.39
Mutation Taster		=100/0	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: rs17483466; hg19: chr2-111797458;