rs2015454

Positions:

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

Variant summary

Our verdict is Benign. Variant got -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

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)

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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
ACOXL	NM_001142807.4	c.1543-3045A>G		intron_variant		ENST00000439055.6
ACOXL-AS1	NR_122074.1	n.70-273T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ACOXL	ENST00000439055.6	c.1543-3045A>G		intron_variant		2	NM_001142807.4
MIR4435-2HG	ENST00000645030.2	n.453-77649T>C		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.776

Gnomad4 AMR AF: 0.405

Gnomad4 ASJ AF: 0.409

Gnomad4 EAS AF: 0.556

Gnomad4 SAS AF: 0.309

Gnomad4 FIN AF: 0.547

Gnomad4 NFE AF: 0.540

Gnomad4 OTH AF: 0.533

Alfa AF: 0.532 Hom.: 10147

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2015454; hg19: chr2-111872148;