rs1439287

Variant names:

• chr2-111114320-G-A
• rs1439287
• NM_001142807.4:c.1543-3296G>A

Your query was ambiguous. Multiple possible variants found:

• chr2-111114320-G-A
• chr2-111114320-G-C
• chr2-111114320-G-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.1543-3296G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.419 in 152,256 control chromosomes in the GnomAD database, including 13,875 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 0.42 (13839 hom., cov: 32)
  • Exomes 𝑓: 0.51 (36 hom.)
• Consequence: ACOXL NM_001142807.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.228
• Publications: 32 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=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.471 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ACOXL	NM_001142807.4	c.1543-3296G>A		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.1543-3296G>A		intron_variant	Intron 17 of 17	2	NM_001142807.4	ENSP00000407761.1

Frequencies

GnomAD3 genomes AF: 0.419 AC: 63588 AN: 151832 Hom.: 13840 Cov.: 32

Gnomad AFR AF: 0.380

Gnomad AMI AF: 0.447

Gnomad AMR AF: 0.288

Gnomad ASJ AF: 0.367

Gnomad EAS AF: 0.429

Gnomad SAS AF: 0.218

Gnomad FIN AF: 0.508

Gnomad MID AF: 0.241

Gnomad NFE AF: 0.476

Gnomad OTH AF: 0.385

GnomAD4 exome AF: 0.513 AC: 157 AN: 306 Hom.: 36 Cov.: 0 AF XY: 0.546 AC XY: 107 AN XY: 196

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.522 AC: 145 AN: 278

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 2

European-Non Finnish (NFE) AF: 0.455 AC: 10 AN: 22

Other (OTH) AF: 0.500 AC: 2 AN: 4

GnomAD4 genome AF: 0.419 AC: 63605 AN: 151950 Hom.: 13839 Cov.: 32 AF XY: 0.413 AC XY: 30668 AN XY: 74266

African (AFR) AF: 0.379 AC: 15710 AN: 41412

American (AMR) AF: 0.287 AC: 4385 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.367 AC: 1274 AN: 3470

East Asian (EAS) AF: 0.428 AC: 2206 AN: 5150

South Asian (SAS) AF: 0.218 AC: 1053 AN: 4826

European-Finnish (FIN) AF: 0.508 AC: 5358 AN: 10550

Middle Eastern (MID) AF: 0.235 AC: 69 AN: 294

European-Non Finnish (NFE) AF: 0.476 AC: 32328 AN: 67960

Other (OTH) AF: 0.387 AC: 815 AN: 2108

Alfa AF: 0.447 Hom.: 49929

Bravo AF: 0.405

Asia WGS AF: 0.315 AC: 1098 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.9
DANN	Benign	0.43
PhyloP100		-0.23
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: rs1439287; hg19: chr2-111871897;