rs60400822
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1
This summary comes from the ClinGen Evidence Repository: The c.478-22_478-21del variant in ACADVL is an intronic variant which occurs in intron 6. The highest population minor allele frequency in gnomAD v2.1.1 is 0.2253 in the African population, which is higher than the ClinGen ACADVL Variant Curation Expert Panel threshold (≥0.007) for BA1, and therefore meets this criterion (BA1). The results from in silico splicing predictors (SpliceAI) support that this variant does not affect splicing (BP4). In summary, this variant meets the criteria to be classified as benign for autosomal recessive very long chain acyl-CoA dehydrogenase (VLCAD) deficiency based on the ACMG/AMP criteria applied, as specified by the ClinGen ACADVL Variant Curation Expert Panel: BA1, BP4. LINK:https://erepo.genome.network/evrepo/ui/classification/CA8337734/MONDO:0008723/021
Frequency
Consequence
NM_000018.4 intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ACADVL | NM_000018.4 | c.478-22_478-21del | intron_variant | ENST00000356839.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ACADVL | ENST00000356839.10 | c.478-22_478-21del | intron_variant | 1 | NM_000018.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0649 AC: 9861AN: 152026Hom.: 1049 Cov.: 31
GnomAD3 exomes AF: 0.0181 AC: 4552AN: 251378Hom.: 399 AF XY: 0.0136 AC XY: 1854AN XY: 135892
GnomAD4 exome AF: 0.00778 AC: 11379AN: 1461780Hom.: 1000 AF XY: 0.00692 AC XY: 5032AN XY: 727194
GnomAD4 genome ? AF: 0.0651 AC: 9900AN: 152144Hom.: 1057 Cov.: 31 AF XY: 0.0624 AC XY: 4642AN XY: 74378
ClinVar
Submissions by phenotype
Very long chain acyl-CoA dehydrogenase deficiency Benign:3
Benign, criteria provided, single submitter | clinical testing | Wong Mito Lab, Molecular and Human Genetics, Baylor College of Medicine | Nov 01, 2019 | The NM_000018.3:c.478-22_478-21delCA (NP_000009.1:p.?) [GRCH38: NC_000017.11:g.7221516_7221517delCA] variant in ACADVL gene is interpretated to be Benign based on ACMG guidelines (PMID: 25741868). This variant has been reported. This variant meets the following evidence codes reported in the ACMG guidelines: BS1, BS2 - |
Benign, criteria provided, single submitter | clinical testing | ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories | Nov 13, 2018 | - - |
Benign, reviewed by expert panel | curation | ClinGen ACADVL Variant Curation Expert Panel, ClinGen | Sep 22, 2022 | The c.478-22_478-21del variant in ACADVL is an intronic variant which occurs in intron 6. The highest population minor allele frequency in gnomAD v2.1.1 is 0.2253 in the African population, which is higher than the ClinGen ACADVL Variant Curation Expert Panel threshold (≥0.007) for BA1, and therefore meets this criterion (BA1). The results from in silico splicing predictors (SpliceAI) support that this variant does not affect splicing (BP4). In summary, this variant meets the criteria to be classified as benign for autosomal recessive very long chain acyl-CoA dehydrogenase (VLCAD) deficiency based on the ACMG/AMP criteria applied, as specified by the ClinGen ACADVL Variant Curation Expert Panel: BA1, BP4. - |
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Mar 03, 2015 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at