rs3789106

Variant names:

• chr2-110963307-T-G
• rs3789106
• NM_001142807.4:c.1060-23801T>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 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]

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 (NFE) allele frequency at 95% confidence interval = 0.43 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ACOXL	NM_001142807.4	c.1060-23801T>G		intron_variant	Intron 12 of 17	ENST00000439055.6	NP_001136279.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ACOXL	ENST00000439055.6	c.1060-23801T>G		intron_variant	Intron 12 of 17	2	NM_001142807.4	ENSP00000407761.1

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

African (AFR) AF: 0.150 AC: 5792 AN: 38708

American (AMR) AF: 0.423 AC: 6193 AN: 14640

Ashkenazi Jewish (ASJ) AF: 0.505 AC: 1747 AN: 3462

East Asian (EAS) AF: 0.166 AC: 670 AN: 4034

South Asian (SAS) AF: 0.362 AC: 1635 AN: 4516

European-Finnish (FIN) AF: 0.344 AC: 3586 AN: 10438

Middle Eastern (MID) AF: 0.510 AC: 150 AN: 294

European-Non Finnish (NFE) AF: 0.434 AC: 29378 AN: 67682

Other (OTH) AF: 0.380 AC: 775 AN: 2040

Alfa AF: 0.416 Hom.: 26781

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
PhyloP100		-1.0
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: rs3789106; hg19: chr2-111720884; COSMIC: COSV67735864; COSMIC: COSV67735864;