rs17671352
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4BA1
This summary comes from the ClinGen Evidence Repository: The c.1605+6T>C variant in ACADVL is an intronic variant which occurs in intron 16. The highest population minor allele frequency in gnomAD v2.1.1 is 0.66 in European Finnish 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 ExpertPanel: BA1, BP4. LINK:https://erepo.genome.network/evrepo/ui/classification/CA274404/MONDO:0008723/021
Frequency
Consequence
NM_000018.4 splice_region, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -9 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.569 AC: 86437AN: 151808Hom.: 25290 Cov.: 31
GnomAD3 exomes AF: 0.598 AC: 149132AN: 249274Hom.: 45629 AF XY: 0.610 AC XY: 82392AN XY: 135080
GnomAD4 exome AF: 0.616 AC: 899884AN: 1461136Hom.: 279411 Cov.: 71 AF XY: 0.620 AC XY: 450287AN XY: 726846
GnomAD4 genome AF: 0.569 AC: 86505AN: 151926Hom.: 25315 Cov.: 31 AF XY: 0.572 AC XY: 42513AN XY: 74260
ClinVar
Submissions by phenotype
Very long chain acyl-CoA dehydrogenase deficiency Benign:8
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The NM_000018.3:c.1605+6T>C (NP_000009.1:p.?) [GRCH38: NC_000017.11:g.7224399T>C] 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 -
This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. -
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The c.1605+6T>C variant in ACADVL is an intronic variant which occurs in intron 16. The highest population minor allele frequency in gnomAD v2.1.1 is 0.66 in European Finnish 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 ExpertPanel: BA1, BP4. -
not specified Benign:6
This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -
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The c.1605+6T>C variant in ACADVL is classified as benign because it has been identified in 59% (167006/280516) of the total chromosomes by gnomAD (http://gnomad.broadinstitute.org). ACMG/AMP Criteria applied: BA1. -
not provided Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at