rs4849360

Variant names:

• chr2-111058294-C-T
• rs4849360
• NM_001142807.4:c.1440+9006C>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.1440+9006C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.887 in 152,216 control chromosomes in the GnomAD database, including 60,171 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 0.89 (60171 hom., cov: 32)
• Consequence: ACOXL NM_001142807.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0550
• Publications: 3 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]

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=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.963 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ACOXL	NM_001142807.4	MANE Select	c.1440+9006C>T		intron	N/A	NP_001136279.1	Q9NUZ1-4
	ACOXL	NM_001437600.1		c.1530+9006C>T		intron	N/A	NP_001424529.1	A0A7I2V3X2
	ACOXL	NM_001371254.1		c.1530+9006C>T		intron	N/A	NP_001358183.1	Q9NUZ1-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ACOXL	ENST00000439055.6	TSL:2 MANE Select	c.1440+9006C>T		intron	N/A	ENSP00000407761.1	Q9NUZ1-4
	ACOXL	ENST00000417074.5	TSL:1	c.954+9006C>T		intron	N/A	ENSP00000387832.1	A0A0C4DG10
	ACOXL	ENST00000957119.1		c.1572+9006C>T		intron	N/A	ENSP00000627178.1

Frequencies

GnomAD3 genomes AF: 0.887 AC: 134939 AN: 152098 Hom.: 60119 Cov.: 32

Gnomad AFR AF: 0.971

Gnomad AMI AF: 0.986

Gnomad AMR AF: 0.817

Gnomad ASJ AF: 0.917

Gnomad EAS AF: 0.777

Gnomad SAS AF: 0.851

Gnomad FIN AF: 0.891

Gnomad MID AF: 0.939

Gnomad NFE AF: 0.859

Gnomad OTH AF: 0.888

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

GnomAD4 genome AF: 0.887 AC: 135044 AN: 152216 Hom.: 60171 Cov.: 32 AF XY: 0.886 AC XY: 65958 AN XY: 74434

African (AFR) AF: 0.971 AC: 40349 AN: 41540

American (AMR) AF: 0.816 AC: 12472 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.917 AC: 3181 AN: 3470

East Asian (EAS) AF: 0.777 AC: 4019 AN: 5174

South Asian (SAS) AF: 0.850 AC: 4102 AN: 4826

European-Finnish (FIN) AF: 0.891 AC: 9449 AN: 10600

Middle Eastern (MID) AF: 0.928 AC: 271 AN: 292

European-Non Finnish (NFE) AF: 0.859 AC: 58420 AN: 68004

Other (OTH) AF: 0.891 AC: 1882 AN: 2112

Alfa AF: 0.878 Hom.: 8449

Bravo AF: 0.884

Asia WGS AF: 0.849 AC: 2952 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	0.93
DANN	Benign	0.53
PhyloP100		-0.055
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: rs4849360; hg19: chr2-111815871;