rs1057518752
Variant summary
Our verdict is Likely pathogenic. Variant got 7 ACMG points: 7P and 0B. PM1PM2PP3_ModeratePP5
The NM_014049.5(ACAD9):āc.1687C>Gā(p.His563Asp) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000137 in 1,461,692 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Pathogenic (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. H563Y) has been classified as Uncertain significance.
Frequency
Consequence
NM_014049.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 7 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ACAD9 | NM_014049.5 | c.1687C>G | p.His563Asp | missense_variant | 16/18 | ENST00000308982.12 | |
CFAP92 | NM_001394090.1 | c.*155G>C | 3_prime_UTR_variant | 16/16 | ENST00000645291.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ACAD9 | ENST00000308982.12 | c.1687C>G | p.His563Asp | missense_variant | 16/18 | 1 | NM_014049.5 | P1 | |
CFAP92 | ENST00000645291.3 | c.*155G>C | 3_prime_UTR_variant | 16/16 | NM_001394090.1 | P2 |
Frequencies
GnomAD3 genomes ? Cov.: 33
GnomAD4 exome AF: 0.00000137 AC: 2AN: 1461692Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 727168
GnomAD4 genome ? Cov.: 33
ClinVar
Submissions by phenotype
Acyl-CoA dehydrogenase 9 deficiency Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | OMIM | Dec 13, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at