rs747580

Variant names:

• chr4-8371361-T-C
• rs747580
• NM_003501.3:c.1897-367A>G

Variant summary

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

The NM_003501.3(ACOX3):​c.1897-367A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.675 in 152,052 control chromosomes in the GnomAD database, including 35,831 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 0.67 (35831 hom., cov: 33)
• Consequence: ACOX3 NM_003501.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0110

Genes affected

ACOX3 (HGNC:121): (acyl-CoA oxidase 3, pristanoyl) Acyl-Coenzyme A oxidase 3 also know as pristanoyl -CoA oxidase (ACOX3)is involved in the desaturation of 2-methyl branched fatty acids in peroxisomes. Unlike the rat homolog, the human gene is expressed in very low amounts in liver such that its mRNA was undetectable by routine Northern-blot analysis or its product by immunoblotting or by enzyme activity measurements. However the human cDNA encoding a 700 amino acid protein with a peroxisomal targeting C-terminal tripeptide S-K-L was isolated and is thought to be expressed under special conditions such as specific developmental stages or in a tissue specific manner in tissues that have not yet been examined. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.847 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ACOX3	NM_003501.3	c.1897-367A>G		intron_variant	Intron 16 of 17	ENST00000356406.10	NP_003492.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ACOX3	ENST00000356406.10	c.1897-367A>G		intron_variant	Intron 16 of 17	1	NM_003501.3	ENSP00000348775.4

Frequencies

GnomAD3 genomes AF: 0.675 AC: 102509 AN: 151934 Hom.: 35791 Cov.: 33

Gnomad AFR AF: 0.855

Gnomad AMI AF: 0.643

Gnomad AMR AF: 0.554

Gnomad ASJ AF: 0.676

Gnomad EAS AF: 0.496

Gnomad SAS AF: 0.683

Gnomad FIN AF: 0.532

Gnomad MID AF: 0.728

Gnomad NFE AF: 0.628

Gnomad OTH AF: 0.664

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

GnomAD4 genome AF: 0.675 AC: 102597 AN: 152052 Hom.: 35831 Cov.: 33 AF XY: 0.667 AC XY: 49589 AN XY: 74296

Gnomad4 AFR AF: 0.855

Gnomad4 AMR AF: 0.553

Gnomad4 ASJ AF: 0.676

Gnomad4 EAS AF: 0.496

Gnomad4 SAS AF: 0.683

Gnomad4 FIN AF: 0.532

Gnomad4 NFE AF: 0.628

Gnomad4 OTH AF: 0.661

Alfa AF: 0.634 Hom.: 50369

Bravo AF: 0.678

Asia WGS AF: 0.572 AC: 1991 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	4.2
DANN	Benign	0.52

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: rs747580; hg19: chr4-8373088;