rs6490294
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_025247.6(ACAD10):c.2818-1138C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.355 in 151,578 control chromosomes in the GnomAD database, including 13,965 homozygotes. 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 0.35 ( 13965 hom., cov: 30)
Exomes 𝑓: 0.19 ( 0 hom. )
Consequence
ACAD10
NM_025247.6 intron
NM_025247.6 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.192
Genes affected
ACAD10 (HGNC:21597): (acyl-CoA dehydrogenase family member 10) This gene encodes a member of the acyl-CoA dehydrogenase family of enzymes (ACADs), which participate in the beta-oxidation of fatty acids in mitochondria. The encoded enzyme contains a hydrolase domain at the N-terminal portion, a serine/threonine protein kinase catlytic domain in the central region, and a conserved ACAD domain at the C-terminus. Several alternatively spliced transcript variants of this gene have been described, but the full-length nature of some of these variants has not been determined. [provided by RefSeq, Nov 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-1.03).
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.834 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ACAD10 | NM_025247.6 | c.2818-1138C>A | intron_variant | ENST00000313698.9 | |||
ACAD10 | NM_001136538.2 | c.2911-1138C>A | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ACAD10 | ENST00000313698.9 | c.2818-1138C>A | intron_variant | 1 | NM_025247.6 | P1 | |||
ACAD10 | ENST00000455480.6 | c.2911-1138C>A | intron_variant | 1 | |||||
ACAD10 | ENST00000508303.5 | n.1888-3034C>A | intron_variant, non_coding_transcript_variant | 2 | |||||
ACAD10 | ENST00000547491.1 | n.601-1138C>A | intron_variant, non_coding_transcript_variant | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.354 AC: 53645AN: 151446Hom.: 13925 Cov.: 30
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GnomAD4 exome AF: 0.188 AC: 3AN: 16Hom.: 0 AF XY: 0.167 AC XY: 2AN XY: 12
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GnomAD4 genome ? AF: 0.355 AC: 53746AN: 151562Hom.: 13965 Cov.: 30 AF XY: 0.354 AC XY: 26255AN XY: 74074
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ClinVar
Not reported inComputational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at