Variant 4-8373615-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BA1

The NM_003501.3(ACOX3):c.1842C>T(p.Ser614Ser) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.139 in 1,611,924 control chromosomes in the GnomAD database, including 16,013 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.14 ( 1503 hom., cov: 32)

Exomes 𝑓: 0.14 ( 14510 hom. )

Consequence

ACOX3
NM_003501.3 synonymous

Scores

Clinical Significance

Benign criteria provided, single submitter B:2

Conservation

PhyloP100: -0.349

Variant links:

Genes affected

ACOX3 (HGNC:121): (acyl-CoA oxidase 3, pristanoyl) Acyl-Coenzyme A oxidase 3 also know as pristanoyl -CoA oxidase (ACOX3)is involved in the desaturation of 2-methyl branched fatty acids in peroxisomes. Unlike the rat homolog, the human gene is expressed in very low amounts in liver such that its mRNA was undetectable by routine Northern-blot analysis or its product by immunoblotting or by enzyme activity measurements. However the human cDNA encoding a 700 amino acid protein with a peroxisomal targeting C-terminal tripeptide S-K-L was isolated and is thought to be expressed under special conditions such as specific developmental stages or in a tissue specific manner in tissues that have not yet been examined. [provided by RefSeq, Jul 2008]

ACOX3 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -15 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.91).

BP6

Variant 4-8373615-G-A is Benign according to our data. Variant chr4-8373615-G-A is described in ClinVar as [Benign]. Clinvar id is 559046.Status of the report is criteria_provided_single_submitter, 1 stars.

BP7

Synonymous conserved (PhyloP=-0.349 with no splicing effect.

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.163 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ACOX3	NM_003501.3 link	c.1842C>T	p.Ser614Ser	synonymous_variant	16/18	ENST00000356406.10	NP_003492.2	O15254-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ACOX3	ENST00000356406.10 link	c.1842C>T	p.Ser614Ser	synonymous_variant	16/18	1	NM_003501.3	ENSP00000348775.4		O15254-1

Frequencies

GnomAD3 genomes

AF:

0.141

AC:

21370

AN:

152090

Hom.:

1501

Cov.:

show subpopulations

Gnomad AFR

AF:

0.165

Gnomad AMI

AF:

0.0647

Gnomad AMR

AF:

0.107

Gnomad ASJ

AF:

0.118

Gnomad EAS

AF:

0.126

Gnomad SAS

AF:

0.171

Gnomad FIN

AF:

0.117

Gnomad MID

AF:

0.161

Gnomad NFE

AF:

0.138

Gnomad OTH

AF:

0.135

GnomAD3 exomes

AF:

0.132

AC:

32428

AN:

246326

Hom.:

2240

AF XY:

0.135

AC XY:

17988

AN XY:

133282

show subpopulations

Gnomad AFR exome

AF:

0.163

Gnomad AMR exome

AF:

0.0762

Gnomad ASJ exome

AF:

0.117

Gnomad EAS exome

AF:

0.135

Gnomad SAS exome

AF:

0.169

Gnomad FIN exome

AF:

0.120

Gnomad NFE exome

AF:

0.136

Gnomad OTH exome

AF:

0.141

GnomAD4 exome

AF:

0.138

AC:

201901

AN:

1459716

Hom.:

14510

Cov.:

AF XY:

0.139

AC XY:

101238

AN XY:

726028

show subpopulations

Gnomad4 AFR exome

AF:

0.171

Gnomad4 AMR exome

AF:

0.0783

Gnomad4 ASJ exome

AF:

0.117

Gnomad4 EAS exome

AF:

0.108

Gnomad4 SAS exome

AF:

0.175

Gnomad4 FIN exome

AF:

0.121

Gnomad4 NFE exome

AF:

0.139

Gnomad4 OTH exome

AF:

0.145

GnomAD4 genome

AF:

0.141

AC:

21392

AN:

152208

Hom.:

1503

Cov.:

AF XY:

0.140

AC XY:

10442

AN XY:

74412

show subpopulations

Gnomad4 AFR

AF:

0.164

Gnomad4 AMR

AF:

0.107

Gnomad4 ASJ

AF:

0.118

Gnomad4 EAS

AF:

0.126

Gnomad4 SAS

AF:

0.172

Gnomad4 FIN

AF:

0.117

Gnomad4 NFE

AF:

0.138

Gnomad4 OTH

AF:

0.135

Alfa

AF:

0.139

Hom.:

768

Bravo

AF:

0.139

Asia WGS

AF:

0.124

AC:

430

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, no assertion criteria provided	clinical testing	Mayo Clinic Laboratories, Mayo Clinic	Dec 15, 2015	- -
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

-0.91

CADD

Benign

0.26

DANN

Benign

0.82

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.090

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