rs4849121

Positions:

• chr2-110842129-G-A
• chr2-110842129-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001142807.4(ACOXL):​c.788+724G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.444 in 151,954 control chromosomes in the GnomAD database, including 15,435 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 0.44 (15435 hom., cov: 31)
• Consequence: ACOXL NM_001142807.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.348

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.521 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ACOXL	NM_001142807.4	c.788+724G>A		intron_variant		ENST00000439055.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ACOXL	ENST00000439055.6	c.788+724G>A		intron_variant		2	NM_001142807.4

Frequencies

GnomAD3 genomes AF: 0.444 AC: 67364 AN: 151836 Hom.: 15413 Cov.: 31

Gnomad AFR AF: 0.326

Gnomad AMI AF: 0.339

Gnomad AMR AF: 0.486

Gnomad ASJ AF: 0.464

Gnomad EAS AF: 0.536

Gnomad SAS AF: 0.537

Gnomad FIN AF: 0.569

Gnomad MID AF: 0.424

Gnomad NFE AF: 0.474

Gnomad OTH AF: 0.426

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

GnomAD4 genome AF: 0.444 AC: 67434 AN: 151954 Hom.: 15435 Cov.: 31 AF XY: 0.448 AC XY: 33304 AN XY: 74268

Gnomad4 AFR AF: 0.326

Gnomad4 AMR AF: 0.486

Gnomad4 ASJ AF: 0.464

Gnomad4 EAS AF: 0.535

Gnomad4 SAS AF: 0.538

Gnomad4 FIN AF: 0.569

Gnomad4 NFE AF: 0.474

Gnomad4 OTH AF: 0.425

Alfa AF: 0.474 Hom.: 38268

Bravo AF: 0.432

Asia WGS AF: 0.511 AC: 1777 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.3
DANN	Benign	0.40

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

Publications

LitVar

Other links and lift over

dbSNP: rs4849121; hg19: chr2-111599706;