rs3789106

chr2-110963307-T-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001142807.4(ACOXL):c.1060-23801T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.343 in 146,722 control chromosomes in the GnomAD database, including 9,778 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 0.34 (9778 hom., cov: 31)
• Consequence: ACOXL NM_001142807.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.03

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.43 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ACOXL	NM_001142807.4	c.1060-23801T>G		intron_variant		ENST00000439055.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ACOXL	ENST00000439055.6	c.1060-23801T>G		intron_variant		2	NM_001142807.4

Frequencies

GnomAD3 genomes AF: 0.344 AC: 50379 AN: 146608 Hom.: 9773 Cov.: 31

Gnomad AFR AF: 0.150

Gnomad AMI AF: 0.513

Gnomad AMR AF: 0.423

Gnomad ASJ AF: 0.505

Gnomad EAS AF: 0.166

Gnomad SAS AF: 0.362

Gnomad FIN AF: 0.344

Gnomad MID AF: 0.509

Gnomad NFE AF: 0.434

Gnomad OTH AF: 0.381

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

GnomAD4 genome AF: 0.343 AC: 50392 AN: 146722 Hom.: 9778 Cov.: 31 AF XY: 0.342 AC XY: 24435 AN XY: 71526

Gnomad4 AFR AF: 0.150

Gnomad4 AMR AF: 0.423

Gnomad4 ASJ AF: 0.505

Gnomad4 EAS AF: 0.166

Gnomad4 SAS AF: 0.362

Gnomad4 FIN AF: 0.344

Gnomad4 NFE AF: 0.434

Gnomad4 OTH AF: 0.380

Alfa AF: 0.424 Hom.: 19980

Bravo AF: 0.327

Asia WGS AF: 0.237 AC: 826 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	0.84
Dann	Benign	0.83

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

Publications

LitVar

Other links and lift over

dbSNP: rs3789106; hg19: chr2-111720884; COSMIC: COSV67735864; COSMIC: COSV67735864;