chr17-7219921-T-TGGGCGTGCAGGACGC
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Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP6_Very_StrongBA1
The ENST00000350303.9(ACADVL):c.-63_-49dup variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.564 in 1,554,922 control chromosomes in the GnomAD database, including 250,780 homozygotes. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.51 ( 20943 hom., cov: 0)
Exomes 𝑓: 0.57 ( 229837 hom. )
Consequence
ACADVL
ENST00000350303.9 5_prime_UTR
ENST00000350303.9 5_prime_UTR
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: -2.14
Genes affected
ACADVL (HGNC:92): (acyl-CoA dehydrogenase very long chain) The protein encoded by this gene is targeted to the inner mitochondrial membrane where it catalyzes the first step of the mitochondrial fatty acid beta-oxidation pathway. This acyl-Coenzyme A dehydrogenase is specific to long-chain and very-long-chain fatty acids. A deficiency in this gene product reduces myocardial fatty acid beta-oxidation and is associated with cardiomyopathy. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -16 ACMG points.
BP6
Variant 17-7219921-T-TGGGCGTGCAGGACGC is Benign according to our data. Variant chr17-7219921-T-TGGGCGTGCAGGACGC is described in ClinVar as [Benign]. Clinvar id is 166637.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.584 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ACADVL | NM_000018.4 | upstream_gene_variant | ENST00000356839.10 | NP_000009.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ACADVL | ENST00000356839.10 | upstream_gene_variant | 1 | NM_000018.4 | ENSP00000349297 | P1 |
Frequencies
GnomAD3 genomes AF: 0.513 AC: 77778AN: 151612Hom.: 20921 Cov.: 0
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GnomAD4 exome AF: 0.569 AC: 798723AN: 1403190Hom.: 229837 Cov.: 99 AF XY: 0.572 AC XY: 396860AN XY: 693630
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GnomAD4 genome AF: 0.513 AC: 77841AN: 151732Hom.: 20943 Cov.: 0 AF XY: 0.518 AC XY: 38438AN XY: 74168
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ClinVar
Significance: Benign
Submissions summary: Benign:4
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
Very long chain acyl-CoA dehydrogenase deficiency Benign:2
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Jul 08, 2021 | - - |
Benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jun 14, 2016 | - - |
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | Eurofins Ntd Llc (ga) | Feb 03, 2014 | - - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jun 23, 2018 | - - |
Computational scores
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Find out detailed SpliceAI scores and Pangolin per-transcript scores at