rs6795193

chr3-58512052-C-T

Variant summary

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

The NM_003500.4(ACOX2):c.1851-3027G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.28 in 152,090 control chromosomes in the GnomAD database, including 6,372 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 0.28 (6372 hom., cov: 32)
• Consequence: ACOX2 NM_003500.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.169

Genes affected

ACOX2 (HGNC:120): (acyl-CoA oxidase 2) The product of this gene belongs to the acyl-CoA oxidase family. It encodes the branched-chain acyl-CoA oxidase which is involved in the degradation of long branched fatty acids and bile acid intermediates in peroxisomes. Deficiency of this enzyme results in the accumulation of branched fatty acids and bile acid intermediates, and may lead to Zellweger syndrome, severe cognitive disability, and death in children. [provided by RefSeq, Mar 2009]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.316 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ACOX2	NM_003500.4	c.1851-3027G>A		intron_variant		ENST00000302819.10
ACOX2	XM_005265505.2	c.1851-3027G>A		intron_variant
ACOX2	XM_006713340.4	c.1557-3027G>A		intron_variant
ACOX2	XM_047449042.1	c.2049-3027G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ACOX2	ENST00000302819.10	c.1851-3027G>A		intron_variant		1	NM_003500.4	P1

Frequencies

GnomAD3 genomes AF: 0.280 AC: 42531 AN: 151972 Hom.: 6369 Cov.: 32

Gnomad AFR AF: 0.277

Gnomad AMI AF: 0.357

Gnomad AMR AF: 0.236

Gnomad ASJ AF: 0.418

Gnomad EAS AF: 0.00269

Gnomad SAS AF: 0.200

Gnomad FIN AF: 0.213

Gnomad MID AF: 0.339

Gnomad NFE AF: 0.320

Gnomad OTH AF: 0.299

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

GnomAD4 genome AF: 0.280 AC: 42555 AN: 152090 Hom.: 6372 Cov.: 32 AF XY: 0.271 AC XY: 20119 AN XY: 74332

Gnomad4 AFR AF: 0.277

Gnomad4 AMR AF: 0.235

Gnomad4 ASJ AF: 0.418

Gnomad4 EAS AF: 0.00270

Gnomad4 SAS AF: 0.200

Gnomad4 FIN AF: 0.213

Gnomad4 NFE AF: 0.320

Gnomad4 OTH AF: 0.296

Alfa AF: 0.322 Hom.: 10676

Bravo AF: 0.284

Asia WGS AF: 0.0990 AC: 348 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
Cadd	Benign	9.4
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: rs6795193; hg19: chr3-58497779;