Evidence Repository - Clinical Genome Resources

The ClinGen Evidence Repository is an FDA-recognized human genetic variant database containing expert-curated assertions regarding variants' pathogenicity and supporting evidence summaries. [Disclaimer]

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Variant: NM_000018.4(ACADVL):c.117C>T (p.Pro39=)

CA8337549

703885 (ClinVar)

Gene: ACADVL

Condition: very long chain acyl-CoA dehydrogenase deficiency

Inheritance Mode: Autosomal recessive inheritance

Link to MONDO

UUID: f061a24c-87cb-4fe3-85cf-a67158bbd154

Approved on: 2022-07-28

Published on: 2022-07-28

HGVS expressions

NM_000018.4:c.117C>T

NM_000018.4(ACADVL):c.117C>T (p.Pro39=)

NC_000017.11:g.7220176C>T

CM000679.2:g.7220176C>T

NC_000017.10:g.7123495C>T

CM000679.1:g.7123495C>T

NC_000017.9:g.7064219C>T

NG_007975.1:g.5343C>T

NG_008391.2:g.4875G>A

ENST00000356839.10:c.117C>T

ENST00000322910.9:c.*72C>T

ENST00000350303.9:c.117C>T

ENST00000356839.9:c.117C>T

ENST00000543245.6:c.186C>T

ENST00000577191.5:n.194C>T

ENST00000577857.5:n.207C>T

ENST00000578269.5:n.224C>T

ENST00000578421.1:n.251C>T

ENST00000579286.5:n.224C>T

ENST00000579886.2:c.117C>T

ENST00000580263.5:n.207C>T

ENST00000581562.5:n.164C>T

ENST00000582056.5:n.207C>T

ENST00000582356.5:n.242C>T

ENST00000583312.5:c.117C>T

ENST00000584103.5:c.117C>T

NM_000018.3:c.117C>T

NM_001033859.2:c.117C>T

NM_001270447.1:c.186C>T

NM_001270448.1:c.-112C>T

NM_001033859.3:c.117C>T

NM_001270447.2:c.186C>T

NM_001270448.2:c.-112C>T

Likely Benign

BP7 BP4

Evidence Links 0

Expert Panel

ACADVL VCEP

Criteria Specification Information

Criteria Specifications for this VCEP

Evidence submitted by expert panel

ACADVL VCEP

The c.117C>T variant is a synonymous (silent) variant (p.Pro39=) which occurs in exon 10. The results from 2 in silico splicing predictors (SpliceAI, MutationTaster) support that this variant does not affect splicing. In addition, it occurs at a nucleotide that is not conserved as shown by the 100 vertebrate Basewise Conservation by PhyloP track in the UCSC genome browser (BP4, BP7). The highest population minor allele frequency in gnomAD v2.1.1 is 0.00009 in the East Asian population, which is lower than the ClinGen ACADVL Variant Curation Expert Panel threshold (<0.001) for PM2_Supporting; however, this is not considered conflicting evidence with BP4 and BP7. In summary, this variant meets the criteria to be classified as likely 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: BP4, BP7 (ACADVL VCEP specifications version 1; approved November 8, 2021)

BP7

This is a silent variant, the nucleotide is not highly conserved, and it is predicted to have no impact on splicing.

BP4

Not predicted by SpliceAI or MutationTaster to alter splicing.

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