rs13388646

Positions:

• chr2-111107338-C-T

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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/exons	MANE	UniProt
ACOXL	NM_001142807.4	c.1543-10278C>T		intron_variant		ENST00000439055.6
ACOXL-AS1	NR_122074.1	n.230-5262G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ACOXL	ENST00000439055.6	c.1543-10278C>T		intron_variant		2	NM_001142807.4
ACOXL-AS1	ENST00000376593.2	n.48-5262G>A		intron_variant, non_coding_transcript_variant		2
MIR4435-2HG	ENST00000645030.2	n.453-70416G>A		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.150

Gnomad4 AMR AF: 0.0557

Gnomad4 ASJ AF: 0.0334

Gnomad4 EAS AF: 0.257

Gnomad4 SAS AF: 0.0614

Gnomad4 FIN AF: 0.0792

Gnomad4 NFE AF: 0.0659

Gnomad4 OTH AF: 0.0767

Alfa AF: 0.0687 Hom.: 782

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13388646; hg19: chr2-111864915;