rs11681263

Variant names:

• chr2-111110433-C-A
• rs11681263
• NM_001142807.4:c.1543-7183C>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.1543-7183C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.211 in 152,176 control chromosomes in the GnomAD database, including 3,550 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 0.21 (3550 hom., cov: 32)
• Consequence: ACOXL NM_001142807.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.139
• Publications: 11 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]

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

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=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.236 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.1543-7183C>A		intron	N/A	NP_001136279.1	Q9NUZ1-4
	ACOXL	NM_001437600.1		c.1633-7183C>A		intron	N/A	NP_001424529.1	A0A7I2V3X2
	ACOXL-AS1	NR_122074.1		n.229+3706G>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ACOXL	ENST00000439055.6	TSL:2 MANE Select	c.1543-7183C>A		intron	N/A	ENSP00000407761.1	Q9NUZ1-4
	ACOXL	ENST00000957119.1		c.1675-7183C>A		intron	N/A	ENSP00000627178.1
	ACOXL	ENST00000957116.1		c.1660-7183C>A		intron	N/A	ENSP00000627175.1

Frequencies

GnomAD3 genomes AF: 0.211 AC: 32090 AN: 152058 Hom.: 3552 Cov.: 32

Gnomad AFR AF: 0.189

Gnomad AMI AF: 0.259

Gnomad AMR AF: 0.141

Gnomad ASJ AF: 0.215

Gnomad EAS AF: 0.164

Gnomad SAS AF: 0.118

Gnomad FIN AF: 0.287

Gnomad MID AF: 0.133

Gnomad NFE AF: 0.239

Gnomad OTH AF: 0.190

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

GnomAD4 genome AF: 0.211 AC: 32087 AN: 152176 Hom.: 3550 Cov.: 32 AF XY: 0.210 AC XY: 15604 AN XY: 74388

African (AFR) AF: 0.188 AC: 7819 AN: 41540

American (AMR) AF: 0.141 AC: 2153 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.215 AC: 745 AN: 3470

East Asian (EAS) AF: 0.164 AC: 847 AN: 5164

South Asian (SAS) AF: 0.119 AC: 574 AN: 4828

European-Finnish (FIN) AF: 0.287 AC: 3027 AN: 10556

Middle Eastern (MID) AF: 0.126 AC: 37 AN: 294

European-Non Finnish (NFE) AF: 0.239 AC: 16252 AN: 68000

Other (OTH) AF: 0.188 AC: 397 AN: 2112

Alfa AF: 0.226 Hom.: 13374

Bravo AF: 0.200

Asia WGS AF: 0.123 AC: 430 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	1.8
DANN	Benign	0.70
PhyloP100		0.14
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs11681263; hg19: chr2-111868010;