rs13388646

Variant names:

• chr2-111107338-C-T
• rs13388646
• NM_001142807.4:c.1543-10278C>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.1543-10278C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0944 in 152,232 control chromosomes in the GnomAD database, including 869 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 0.094 (869 hom., cov: 33)
• Consequence: ACOXL NM_001142807.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.360
• Publications: 6 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=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.245 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ACOXL	NM_001142807.4	c.1543-10278C>T		intron_variant	Intron 17 of 17	ENST00000439055.6	NP_001136279.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ACOXL	ENST00000439055.6	c.1543-10278C>T		intron_variant	Intron 17 of 17	2	NM_001142807.4	ENSP00000407761.1

Frequencies

GnomAD3 genomes AF: 0.0943 AC: 14348 AN: 152114 Hom.: 865 Cov.: 33

Gnomad AFR AF: 0.150

Gnomad AMI AF: 0.0559

Gnomad AMR AF: 0.0557

Gnomad ASJ AF: 0.0334

Gnomad EAS AF: 0.257

Gnomad SAS AF: 0.0621

Gnomad FIN AF: 0.0792

Gnomad MID AF: 0.0158

Gnomad NFE AF: 0.0658

Gnomad OTH AF: 0.0718

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

GnomAD4 genome AF: 0.0944 AC: 14371 AN: 152232 Hom.: 869 Cov.: 33 AF XY: 0.0933 AC XY: 6939 AN XY: 74412

African (AFR) AF: 0.150 AC: 6238 AN: 41504

American (AMR) AF: 0.0557 AC: 853 AN: 15308

Ashkenazi Jewish (ASJ) AF: 0.0334 AC: 116 AN: 3470

East Asian (EAS) AF: 0.257 AC: 1331 AN: 5182

South Asian (SAS) AF: 0.0614 AC: 296 AN: 4824

European-Finnish (FIN) AF: 0.0792 AC: 839 AN: 10598

Middle Eastern (MID) AF: 0.0170 AC: 5 AN: 294

European-Non Finnish (NFE) AF: 0.0659 AC: 4480 AN: 68028

Other (OTH) AF: 0.0767 AC: 162 AN: 2112

Alfa AF: 0.0751 Hom.: 2016

Bravo AF: 0.0985

Asia WGS AF: 0.160 AC: 554 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.69
DANN	Benign	0.24
PhyloP100		-0.36
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: rs13388646; hg19: chr2-111864915;