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Variant: NM_000018.4(ACADVL):c.753-2A>G

CA397723611

932844 (ClinVar)

Gene: ACADVL
Condition: very long chain acyl-CoA dehydrogenase deficiency
Inheritance Mode: Autosomal recessive inheritance
UUID: f6184d31-e62e-45e1-8909-b5c0c8836cc6

HGVS expressions

NM_000018.4:c.753-2A>G
NM_000018.4(ACADVL):c.753-2A>G
NC_000017.11:g.7222175A>G
CM000679.2:g.7222175A>G
NC_000017.10:g.7125494A>G
CM000679.1:g.7125494A>G
NC_000017.9:g.7066218A>G
NG_007975.1:g.7342A>G
NG_008391.2:g.2876T>C
ENST00000356839.10:c.753-2A>G
ENST00000322910.9:c.*708-2A>G
ENST00000350303.9:c.687-2A>G
ENST00000356839.9:c.753-2A>G
ENST00000543245.6:c.822-2A>G
ENST00000577191.5:n.923A>G
ENST00000581378.5:n.471-2A>G
ENST00000582379.1:n.137-2A>G
NM_000018.3:c.753-2A>G
NM_001033859.2:c.687-2A>G
NM_001270447.1:c.822-2A>G
NM_001270448.1:c.525-2A>G
NM_001033859.3:c.687-2A>G
NM_001270447.2:c.822-2A>G
NM_001270448.2:c.525-2A>G

Likely Pathogenic

The Expert Panel has overridden the computationally generated classification - "Uncertain Significance - Insufficient Evidence"
Met criteria codes 3
PS1 PVS1_Moderate PM2_Supporting
Not Met criteria codes 9
PM5 PM4 BA1 BP7 BP3 BP4 BP1 BS1 PP2

Evidence Links 0

Expert Panel

Criteria Specification Information

Criteria Specifications for this VCEP
Evidence submitted by expert panel
ACADVL VCEP
The NM_000018.4(ACADVL):c.753-2A>G variant in ACADVL occurs within the canonical splice acceptor site (-2) of intron 8. It is predicted to cause skipping of biologically-relevant-exon 9/20, resulting in an in-frame deletion (removes amino acids Ser-His) that is predicted to escape nonsense mediated decay and remove <10% of the protein (PVS1_Moderate; PMIDs 9973285, 11590124). However, a different nucleotide change at the same position within the canonical splice acceptor site of intron 8 [c.753-2A>C; ClinVar ID: 92290] is classified as likely pathogenic for very long chain acyl CoA dehydrogenase (VLCAD) deficiency by the ClinGen ACADVL Variant Curation Expert Panel (PS1). At least one individual with this variant was identified by newborn screen, but this information is insufficient for to use toward classification (PMID: 26385305). This variant is absent from gnomAD v2.1.1 (PM2_Supporting). Due to conflicting evidence, this variant is classified as a variant of uncertain significance 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: PS1, PVS1_Moderate, PM2_Supporting.
Met criteria codes
PS1
A different nucleotide change at the same position within the canonical splice acceptor site of intron 8 [c.753-2A>C; ClinVar ID: 92290] is classified as likely pathogenic for very long chain acyl CoA dehydrogenase (VLCAD) deficiency by the ClinGen ACADVL Variant Curation Expert Panel (PS1).
PVS1_Moderate
The NM_000018.4(ACADVL):c.753-2A>G variant in ACADVL occurs within the canonical splice acceptor site (-2) of intron 8. It is predicted to cause skipping of biologically-relevant-exon 9/20, resulting in an in-frame deletion (removes amino acids Ser-His) that is predicted to escape nonsense mediated decay (PVS1_Moderate; PMIDs 9973285, 11590124).
PM2_Supporting
This variant is absent from gnomAD v2.1.1 (PM2_Supporting).
Not Met criteria codes
PM5
PM5 is not met; variant is located at 3' splice site
PM4
PM4 is not met
BA1
BA1 is not met
BP7
BP7 is not met
BP3
BP3 is not met
BP4
BP4 is not met
BP1
BP1 is not met
BS1
BS1 is not met
PP2
PP2 is not met
Approved on: 2023-05-23
Published on: 2023-05-23
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