Variant chr3-58530656-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_003500.4(ACOX2):c.820-18C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.415 in 1,607,502 control chromosomes in the GnomAD database, including 147,604 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.31 ( 9445 hom., cov: 34)

Exomes 𝑓: 0.43 ( 138159 hom. )

Consequence

ACOX2
NM_003500.4 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 0.0880

Variant links:

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]

ACOX2 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.88).

BP6

Variant 3-58530656-G-A is Benign according to our data. Variant chr3-58530656-G-A is described in ClinVar as [Benign]. Clinvar id is 1667807.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.442 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	MANE	Protein
ACOX2	NM_003500.4 linkuse as main transcript	c.820-18C>T	intron_variant	ENST00000302819.10	NP_003491.1
ACOX2	XM_005265505.2 linkuse as main transcript	c.820-18C>T	intron_variant		XP_005265562.1
ACOX2	XM_006713340.4 linkuse as main transcript	c.526-18C>T	intron_variant		XP_006713403.1
ACOX2	XM_047449042.1 linkuse as main transcript	c.1018-18C>T	intron_variant		XP_047304998.1

Ensembl

Gene	Transcript	HGVSc	Effect	TSL	MANE	Protein	Appris
ACOX2	ENST00000302819.10 linkuse as main transcript	c.820-18C>T	intron_variant	1	NM_003500.4	ENSP00000307697	P1
ACOX2	ENST00000459701.6 linkuse as main transcript	c.778-18C>T	intron_variant	5		ENSP00000418562
ACOX2	ENST00000489472.1 linkuse as main transcript	c.*47+595C>T	intron_variant, NMD_transcript_variant	5		ENSP00000418515

Frequencies

GnomAD3 genomes

AF:

0.313

AC:

47664

AN:

152104

Hom.:

9442

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0860

Gnomad AMI

AF:

0.478

Gnomad AMR

AF:

0.339

Gnomad ASJ

AF:

0.482

Gnomad EAS

AF:

0.0988

Gnomad SAS

AF:

0.322

Gnomad FIN

AF:

0.337

Gnomad MID

AF:

0.424

Gnomad NFE

AF:

0.446

Gnomad OTH

AF:

0.345

GnomAD3 exomes

AF:

0.361

AC:

88016

AN:

243814

Hom.:

17500

AF XY:

0.369

AC XY:

48577

AN XY:

131540

show subpopulations

Gnomad AFR exome

AF:

0.0779

Gnomad AMR exome

AF:

0.358

Gnomad ASJ exome

AF:

0.476

Gnomad EAS exome

AF:

0.0982

Gnomad SAS exome

AF:

0.347

Gnomad FIN exome

AF:

0.334

Gnomad NFE exome

AF:

0.443

Gnomad OTH exome

AF:

0.401

GnomAD4 exome

AF:

0.426

AC:

619691

AN:

1455280

Hom.:

138159

Cov.:

AF XY:

0.425

AC XY:

307192

AN XY:

723140

show subpopulations

Gnomad4 AFR exome

AF:

0.0696

Gnomad4 AMR exome

AF:

0.354

Gnomad4 ASJ exome

AF:

0.477

Gnomad4 EAS exome

AF:

0.112

Gnomad4 SAS exome

AF:

0.350

Gnomad4 FIN exome

AF:

0.340

Gnomad4 NFE exome

AF:

0.461

Gnomad4 OTH exome

AF:

0.400

GnomAD4 genome

AF:

0.313

AC:

47667

AN:

152222

Hom.:

9445

Cov.:

AF XY:

0.308

AC XY:

22944

AN XY:

74412

show subpopulations

Gnomad4 AFR

AF:

0.0858

Gnomad4 AMR

AF:

0.339

Gnomad4 ASJ

AF:

0.482

Gnomad4 EAS

AF:

0.0993

Gnomad4 SAS

AF:

0.322

Gnomad4 FIN

AF:

0.337

Gnomad4 NFE

AF:

0.446

Gnomad4 OTH

AF:

0.341

Alfa

AF:

0.430

Hom.:

19466

Bravo

AF:

0.306

Asia WGS

AF:

0.212

AC:

739

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Feb 01, 2024	- -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.88

CADD

Benign

1.7

DANN

Benign

0.51

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over