rs875989865
Variant names:
Your query was ambiguous. Multiple possible variants found:
Variant summary
Our verdict is Pathogenic. Variant got 12 ACMG points: 12P and 0B. PVS1PS1_ModeratePM2
The NM_000016.6(ACADM):c.-6_6delGCCAACATGGCAinsACCCCGAAGG(p.Met1fs) variant causes a frameshift, start lost change. The variant was absent in control chromosomes in GnomAD project. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: not found (cov: 32)
Consequence
ACADM
NM_000016.6 frameshift, start_lost
NM_000016.6 frameshift, start_lost
Scores
Not classified
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 3.58
Genes affected
ACADM (HGNC:89): (acyl-CoA dehydrogenase medium chain) This gene encodes the medium-chain specific (C4 to C12 straight chain) acyl-Coenzyme A dehydrogenase. The homotetramer enzyme catalyzes the initial step of the mitochondrial fatty acid beta-oxidation pathway. Defects in this gene cause medium-chain acyl-CoA dehydrogenase deficiency, a disease characterized by hepatic dysfunction, fasting hypoglycemia, and encephalopathy, which can result in infantile death. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Pathogenic. Variant got 12 ACMG points.
PVS1
Loss of function variant, product does not undergo nonsense mediated mRNA decay. Variant located near the start codon (<100nt), not predicted to undergo nonsense mediated mRNA decay. There are 243 pathogenic variants in the truncated region.
PS1
Another start lost variant in NM_000016.6 (ACADM) was described as [Likely_pathogenic] in ClinVar as 555765
PM2
Very rare variant in population databases, with high coverage;
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ACADM | NM_000016.6 | c.-6_6delGCCAACATGGCAinsACCCCGAAGG | p.Met1fs | frameshift_variant, start_lost | Exon 1 of 12 | ENST00000370841.9 | NP_000007.1 | |
ACADM | NM_000016.6 | c.-6_6delGCCAACATGGCAinsACCCCGAAGG | 5_prime_UTR_variant | Exon 1 of 12 | ENST00000370841.9 | NP_000007.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ACADM | ENST00000370841.9 | c.-6_6delGCCAACATGGCAinsACCCCGAAGG | p.Met1fs | frameshift_variant, start_lost | Exon 1 of 12 | 1 | NM_000016.6 | ENSP00000359878.5 | ||
ACADM | ENST00000370841 | c.-6_6delGCCAACATGGCAinsACCCCGAAGG | 5_prime_UTR_variant | Exon 1 of 12 | 1 | NM_000016.6 | ENSP00000359878.5 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 genomes
Cov.:
32
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome Cov.: 32
GnomAD4 genome
Cov.:
32
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at