chr17-75941915-CAT-C
Position:
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BS1_SupportingBS2
The NM_004035.7(ACOX1):c.*4831_*4832del variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00569 in 152,296 control chromosomes in the GnomAD database, including 11 homozygotes. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: 𝑓 0.0057 ( 11 hom., cov: 32)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
ACOX1
NM_004035.7 3_prime_UTR
NM_004035.7 3_prime_UTR
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 2.45
Genes affected
ACOX1 (HGNC:119): (acyl-CoA oxidase 1) The protein encoded by this gene is the first enzyme of the fatty acid beta-oxidation pathway, which catalyzes the desaturation of acyl-CoAs to 2-trans-enoyl-CoAs. It donates electrons directly to molecular oxygen, thereby producing hydrogen peroxide. Defects in this gene result in pseudoneonatal adrenoleukodystrophy, a disease that is characterized by accumulation of very long chain fatty acids. Alternatively spliced transcript variants encoding different isoforms have been identified. [provided by RefSeq, Jul 2008]
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -5 ACMG points.
BS1
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00569 (866/152296) while in subpopulation AFR AF= 0.0195 (810/41552). AF 95% confidence interval is 0.0184. There are 11 homozygotes in gnomad4. There are 421 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck. Existence of Clinvar submissions makes me limit the strength of this signal to Supporting
BS2
High AC in GnomAd4 at 866 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ACOX1 | NM_004035.7 | c.*4831_*4832del | 3_prime_UTR_variant | 14/14 | ENST00000293217.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ACOX1 | ENST00000293217.10 | c.*4831_*4832del | 3_prime_UTR_variant | 14/14 | 1 | NM_004035.7 | A1 | ||
ACOX1 | ENST00000301608.9 | c.*4831_*4832del | 3_prime_UTR_variant | 14/14 | 1 | P3 |
Frequencies
GnomAD3 genomes AF: 0.00566 AC: 861AN: 152178Hom.: 11 Cov.: 32
GnomAD3 genomes
AF:
AC:
861
AN:
152178
Hom.:
Cov.:
32
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 2Hom.: 0 AC XY: 0AN XY: 0
GnomAD4 exome
Data not reliable, filtered out with message: AC0
AF:
AC:
0
AN:
2
Hom.:
AC XY:
0
AN XY:
0
Gnomad4 NFE exome
AF:
GnomAD4 genome AF: 0.00569 AC: 866AN: 152296Hom.: 11 Cov.: 32 AF XY: 0.00565 AC XY: 421AN XY: 74482
GnomAD4 genome
AF:
AC:
866
AN:
152296
Hom.:
Cov.:
32
AF XY:
AC XY:
421
AN XY:
74482
Gnomad4 AFR
AF:
Gnomad4 AMR
AF:
Gnomad4 ASJ
AF:
Gnomad4 EAS
AF:
Gnomad4 SAS
AF:
Gnomad4 FIN
AF:
Gnomad4 NFE
AF:
Gnomad4 OTH
AF:
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
3
AN:
3478
ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Acyl-CoA oxidase deficiency Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jun 14, 2016 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at