rs6732565

Positions:

• chr2-110850255-A-G
• chr2-110850255-A-T

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The NM_001142807.4(ACOXL):​c.788+8850A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.384 in 152,086 control chromosomes in the GnomAD database, including 11,514 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 0.38 (11514 hom., cov: 32)
• Consequence: ACOXL NM_001142807.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.102

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 -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.42).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.556 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ACOXL	NM_001142807.4	c.788+8850A>G		intron_variant		ENST00000439055.6	NP_001136279.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ACOXL	ENST00000439055.6	c.788+8850A>G		intron_variant		2	NM_001142807.4	ENSP00000407761

Frequencies

GnomAD3 genomes AF: 0.384 AC: 58393 AN: 151968 Hom.: 11485 Cov.: 32

Gnomad AFR AF: 0.333

Gnomad AMI AF: 0.400

Gnomad AMR AF: 0.453

Gnomad ASJ AF: 0.375

Gnomad EAS AF: 0.391

Gnomad SAS AF: 0.576

Gnomad FIN AF: 0.406

Gnomad MID AF: 0.394

Gnomad NFE AF: 0.383

Gnomad OTH AF: 0.376

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

GnomAD4 genome AF: 0.384 AC: 58456 AN: 152086 Hom.: 11514 Cov.: 32 AF XY: 0.389 AC XY: 28893 AN XY: 74342

Gnomad4 AFR AF: 0.334

Gnomad4 AMR AF: 0.454

Gnomad4 ASJ AF: 0.375

Gnomad4 EAS AF: 0.391

Gnomad4 SAS AF: 0.573

Gnomad4 FIN AF: 0.406

Gnomad4 NFE AF: 0.383

Gnomad4 OTH AF: 0.380

Alfa AF: 0.386 Hom.: 1465

Bravo AF: 0.383

Asia WGS AF: 0.536 AC: 1865 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.42
CADD	Benign	17
DANN	Benign	0.82

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: rs6732565; hg19: chr2-111607832;