rs4849121

Variant names:

• chr2-110842129-G-A
• rs4849121
• NM_001142807.4:c.788+724G>A

Your query was ambiguous. Multiple possible variants found:

• chr2-110842129-G-A
• chr2-110842129-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.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
• Publications: 15 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=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.521 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.788+724G>A		intron	N/A	NP_001136279.1
	ACOXL	NM_001437600.1		c.788+724G>A		intron	N/A	NP_001424529.1
	ACOXL	NM_001371254.1		c.788+724G>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.788+724G>A		intron	N/A	ENSP00000407761.1
	ACOXL	ENST00000417074.5	TSL:1	c.302+724G>A		intron	N/A	ENSP00000387832.1
	ACOXL	ENST00000340561.8	TSL:1	c.788+724G>A		intron	N/A	ENSP00000343717.4

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

African (AFR) AF: 0.326 AC: 13525 AN: 41434

American (AMR) AF: 0.486 AC: 7418 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.464 AC: 1611 AN: 3470

East Asian (EAS) AF: 0.535 AC: 2758 AN: 5154

South Asian (SAS) AF: 0.538 AC: 2589 AN: 4810

European-Finnish (FIN) AF: 0.569 AC: 6015 AN: 10562

Middle Eastern (MID) AF: 0.412 AC: 121 AN: 294

European-Non Finnish (NFE) AF: 0.474 AC: 32191 AN: 67948

Other (OTH) AF: 0.425 AC: 898 AN: 2112

Alfa AF: 0.467 Hom.: 74988

Bravo AF: 0.432

Asia WGS AF: 0.511 AC: 1777 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.3
DANN	Benign	0.40
PhyloP100		-0.35
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: rs4849121; hg19: chr2-111599706;