rs6732565

Variant names:

• chr2-110850255-A-G
• rs6732565
• NM_001142807.4:c.788+8850A>G

Your query was ambiguous. Multiple possible variants found:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 24 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 -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001142807.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ACOXL	NM_001142807.4	MANE Select	c.788+8850A>G		intron	N/A	NP_001136279.1	Q9NUZ1-4
	ACOXL	NM_001437600.1		c.788+8850A>G		intron	N/A	NP_001424529.1	A0A7I2V3X2
	ACOXL	NM_001371254.1		c.788+8850A>G		intron	N/A	NP_001358183.1	Q9NUZ1-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ACOXL	ENST00000439055.6	TSL:2 MANE Select	c.788+8850A>G		intron	N/A	ENSP00000407761.1	Q9NUZ1-4
	ACOXL	ENST00000417074.5	TSL:1	c.302+8850A>G		intron	N/A	ENSP00000387832.1	A0A0C4DG10
	ACOXL	ENST00000340561.8	TSL:1	c.788+8850A>G		intron	N/A	ENSP00000343717.4	Q9NUZ1-3

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

African (AFR) AF: 0.334 AC: 13856 AN: 41498

American (AMR) AF: 0.454 AC: 6929 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.375 AC: 1299 AN: 3466

East Asian (EAS) AF: 0.391 AC: 2026 AN: 5180

South Asian (SAS) AF: 0.573 AC: 2758 AN: 4810

European-Finnish (FIN) AF: 0.406 AC: 4294 AN: 10584

Middle Eastern (MID) AF: 0.390 AC: 113 AN: 290

European-Non Finnish (NFE) AF: 0.383 AC: 26016 AN: 67970

Other (OTH) AF: 0.380 AC: 800 AN: 2106

Alfa AF: 0.386 Hom.: 18319

Bravo AF: 0.383

Asia WGS AF: 0.536 AC: 1865 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.42
CADD	Benign	17
DANN	Benign	0.82
PhyloP100		0.10
Mutation Taster		=99/1	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: rs6732565; hg19: chr2-111607832;