12-120739407-C-T
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Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_000017.4(ACADS):c.1198C>T(p.Leu400Leu) variant causes a synonymous change. The variant allele was found at a frequency of 0.00000186 in 1,612,202 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.0000066 ( 0 hom., cov: 33)
Exomes 𝑓: 0.0000014 ( 0 hom. )
Consequence
ACADS
NM_000017.4 synonymous
NM_000017.4 synonymous
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 4.76
Genes affected
ACADS (HGNC:90): (acyl-CoA dehydrogenase short chain) This gene encodes a tetrameric mitochondrial flavoprotein, which is a member of the acyl-CoA dehydrogenase family. This enzyme catalyzes the initial step of the mitochondrial fatty acid beta-oxidation pathway. Mutations in this gene have been associated with short-chain acyl-CoA dehydrogenase (SCAD) deficiency. Alternative splicing results in two variants which encode different isoforms. [provided by RefSeq, Oct 2014]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 0 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.22).
Transcripts
RefSeq
| Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|
| ACADS | NM_000017.4 | c.1198C>T | p.Leu400Leu | synonymous_variant | 10/10 | ENST00000242592.9 | NP_000008.1 | |
| ACADS | NM_001302554.2 | c.1186C>T | p.Leu396Leu | synonymous_variant | 10/10 | NP_001289483.1 |
Ensembl
| Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
|---|---|---|---|---|---|---|---|---|---|---|
| ACADS | ENST00000242592.9 | c.1198C>T | p.Leu400Leu | synonymous_variant | 10/10 | 1 | NM_000017.4 | ENSP00000242592.4 | ||
| ACADS | ENST00000411593.2 | c.1186C>T | p.Leu396Leu | synonymous_variant | 10/10 | 2 | ENSP00000401045.2 |
Frequencies
GnomAD3 genomes 0.00000657 AC: 1AN: 152188Hom.: 0 Cov.: 33
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GnomAD3 exomes AF: 0.00000815 AC: 2AN: 245256Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 134032
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GnomAD4 exome AF: 0.00000137 AC: 2AN: 1460014Hom.: 0 Cov.: 33 AF XY: 0.00000138 AC XY: 1AN XY: 726382
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GnomAD4 genome 0.00000657 AC: 1AN: 152188Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 74352
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Not reported inComputational scores
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at