rs2015454

Variant names:

• chr2-111114571-A-G
• rs2015454
• NM_001142807.4:c.1543-3045A>G

Your query was ambiguous. Multiple possible variants found:

• chr2-111114571-A-G
• chr2-111114571-A-T

Variant summary

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

The NM_001142807.4(ACOXL):​c.1543-3045A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.581 in 151,898 control chromosomes in the GnomAD database, including 27,127 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 0.58 (27127 hom., cov: 31)
• Consequence: ACOXL NM_001142807.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.134
• Publications: 11 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]

ACOXL-AS1 (HGNC:41112): (ACOXL antisense RNA 1)

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

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.769 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ACOXL	NM_001142807.4	c.1543-3045A>G		intron_variant	Intron 17 of 17	ENST00000439055.6	NP_001136279.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ACOXL	ENST00000439055.6	c.1543-3045A>G		intron_variant	Intron 17 of 17	2	NM_001142807.4	ENSP00000407761.1

Frequencies

GnomAD3 genomes AF: 0.581 AC: 88150 AN: 151780 Hom.: 27081 Cov.: 31

Gnomad AFR AF: 0.775

Gnomad AMI AF: 0.566

Gnomad AMR AF: 0.406

Gnomad ASJ AF: 0.409

Gnomad EAS AF: 0.556

Gnomad SAS AF: 0.309

Gnomad FIN AF: 0.547

Gnomad MID AF: 0.354

Gnomad NFE AF: 0.540

Gnomad OTH AF: 0.533

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

GnomAD4 genome AF: 0.581 AC: 88247 AN: 151898 Hom.: 27127 Cov.: 31 AF XY: 0.573 AC XY: 42528 AN XY: 74232

African (AFR) AF: 0.776 AC: 32134 AN: 41430

American (AMR) AF: 0.405 AC: 6179 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.409 AC: 1418 AN: 3466

East Asian (EAS) AF: 0.556 AC: 2874 AN: 5168

South Asian (SAS) AF: 0.309 AC: 1488 AN: 4810

European-Finnish (FIN) AF: 0.547 AC: 5759 AN: 10536

Middle Eastern (MID) AF: 0.354 AC: 104 AN: 294

European-Non Finnish (NFE) AF: 0.540 AC: 36653 AN: 67924

Other (OTH) AF: 0.533 AC: 1124 AN: 2110

Alfa AF: 0.532 Hom.: 11306

Bravo AF: 0.584

Asia WGS AF: 0.420 AC: 1463 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	3.1
DANN	Benign	0.49
PhyloP100		0.13
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs2015454; hg19: chr2-111872148;