Genetic Variant ACOXL:c.1543-3296G>A (chr2-111114320-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001142807.4(ACOXL):c.1543-3296G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.419 in 152,256 control chromosomes in the GnomAD database, including 13,875 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 0.42 ( 13839 hom., cov: 32)

Exomes 𝑓: 0.51 ( 36 hom. )

Consequence

ACOXL
NM_001142807.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.228

Publications

32 publications found

Variant links:

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]

ACOXL links:

ACOXL-AS1 (HGNC:41112): (ACOXL antisense RNA 1)

ACOXL-AS1 links:

MIR4435-2HG (HGNC:35163): (MIR4435-2 host gene)

MIR4435-2HG links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.92).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.471 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

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
ACOXL	NM_001142807.4	MANE Select	c.1543-3296G>A	intron	N/A	NP_001136279.1
ACOXL	NM_001437600.1		c.1633-3296G>A	intron	N/A	NP_001424529.1
ACOXL-AS1	NR_122074.1		n.70-22C>T	intron	N/A

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
ACOXL	ENST00000439055.6	TSL:2 MANE Select	c.1543-3296G>A	intron	N/A	ENSP00000407761.1
ACOXL-AS1	ENST00000670010.1		n.2088C>T	non_coding_transcript_exon	Exon 1 of 2
ACOXL	ENST00000676595.2		c.1633-3296G>A	intron	N/A	ENSP00000503683.1

Frequencies

GnomAD3 genomes

AF:

0.419

AC:

63588

AN:

151832

Hom.:

13840

Cov.:

show subpopulations

Gnomad AFR

AF:

0.380

Gnomad AMI

AF:

0.447

Gnomad AMR

AF:

0.288

Gnomad ASJ

AF:

0.367

Gnomad EAS

AF:

0.429

Gnomad SAS

AF:

0.218

Gnomad FIN

AF:

0.508

Gnomad MID

AF:

0.241

Gnomad NFE

AF:

0.476

Gnomad OTH

AF:

0.385

GnomAD4 exome

AF:

0.513

AC:

157

AN:

306

Hom.:

Cov.:

AF XY:

0.546

AC XY:

107

AN XY:

196

show subpopulations

African (AFR)

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AF:

0.522

AC:

145

AN:

278

Middle Eastern (MID)

AF:

0.00

AC:

AN:

European-Non Finnish (NFE)

AF:

0.455

AC:

AN:

Other (OTH)

AF:

0.500

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.419

AC:

63605

AN:

151950

Hom.:

13839

Cov.:

AF XY:

0.413

AC XY:

30668

AN XY:

74266

show subpopulations

African (AFR)

AF:

0.379

AC:

15710

AN:

41412

American (AMR)

AF:

0.287

AC:

4385

AN:

15270

Ashkenazi Jewish (ASJ)

AF:

0.367

AC:

1274

AN:

3470

East Asian (EAS)

AF:

0.428

AC:

2206

AN:

5150

South Asian (SAS)

AF:

0.218

AC:

1053

AN:

4826

European-Finnish (FIN)

AF:

0.508

AC:

5358

AN:

10550

Middle Eastern (MID)

AF:

0.235

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.476

AC:

32328

AN:

67960

Other (OTH)

AF:

0.387

AC:

815

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1867

3734

5600

7467

9334

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

598

1196

1794

2392

2990

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.447

Hom.:

49929

Bravo

AF:

0.405

Asia WGS

AF:

0.315

AC:

1098

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.92

CADD

Benign

1.9

(source)

DANN

Benign

0.43

PhyloP100

-0.23

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over