2-110948161-G-A

Variant names:

• chr2-110948161-G-A
• rs729386
• NM_001142807.4:c.1059+14519G>A

Variant summary

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

The NM_001142807.4(ACOXL):​c.1059+14519G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.674 in 152,124 control chromosomes in the GnomAD database, including 34,795 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 0.67 (34795 hom., cov: 33)
• Consequence: ACOXL NM_001142807.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.188
• Publications: 5 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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.772 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001142807.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ACOXL	NM_001142807.4	MANE Select	c.1059+14519G>A		intron	N/A	NP_001136279.1
	ACOXL	NM_001437600.1		c.1059+14519G>A		intron	N/A	NP_001424529.1
	ACOXL	NM_001371254.1		c.1059+14519G>A		intron	N/A	NP_001358183.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ACOXL	ENST00000439055.6	TSL:2 MANE Select	c.1059+14519G>A		intron	N/A	ENSP00000407761.1
	ACOXL	ENST00000417074.5	TSL:1	c.573+14519G>A		intron	N/A	ENSP00000387832.1
	ACOXL	ENST00000676595.2		c.1059+14519G>A		intron	N/A	ENSP00000503683.1

Frequencies

GnomAD3 genomes AF: 0.674 AC: 102428 AN: 152006 Hom.: 34751 Cov.: 33

Gnomad AFR AF: 0.596

Gnomad AMI AF: 0.643

Gnomad AMR AF: 0.735

Gnomad ASJ AF: 0.739

Gnomad EAS AF: 0.793

Gnomad SAS AF: 0.772

Gnomad FIN AF: 0.688

Gnomad MID AF: 0.728

Gnomad NFE AF: 0.686

Gnomad OTH AF: 0.674

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

GnomAD4 genome AF: 0.674 AC: 102528 AN: 152124 Hom.: 34795 Cov.: 33 AF XY: 0.677 AC XY: 50355 AN XY: 74370

African (AFR) AF: 0.597 AC: 24758 AN: 41488

American (AMR) AF: 0.735 AC: 11249 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.739 AC: 2565 AN: 3470

East Asian (EAS) AF: 0.792 AC: 4104 AN: 5182

South Asian (SAS) AF: 0.771 AC: 3707 AN: 4810

European-Finnish (FIN) AF: 0.688 AC: 7275 AN: 10572

Middle Eastern (MID) AF: 0.728 AC: 214 AN: 294

European-Non Finnish (NFE) AF: 0.686 AC: 46643 AN: 67978

Other (OTH) AF: 0.674 AC: 1427 AN: 2116

Alfa AF: 0.691 Hom.: 20457

Bravo AF: 0.674

Asia WGS AF: 0.752 AC: 2618 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.31
DANN	Benign	0.63
PhyloP100		-0.19
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: rs729386; hg19: chr2-111705738;