11-108121200-CAAAAAA-CAAA
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1
The NM_001386681.1(ACAT1):c.-199+4313_-199+4315delAAA variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0921 in 249,200 control chromosomes in the GnomAD database, including 21 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.010 ( 19 hom., cov: 0)
Exomes 𝑓: 0.20 ( 2 hom. )
Consequence
ACAT1
NM_001386681.1 intron
NM_001386681.1 intron
Scores
Not classified
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.702
Genes affected
ACAT1 (HGNC:93): (acetyl-CoA acetyltransferase 1) This gene encodes a mitochondrially localized enzyme that catalyzes the reversible formation of acetoacetyl-CoA from two molecules of acetyl-CoA. Defects in this gene are associated with 3-ketothiolase deficiency, an inborn error of isoleucine catabolism characterized by urinary excretion of 2-methyl-3-hydroxybutyric acid, 2-methylacetoacetic acid, tiglylglycine, and butanone. [provided by RefSeq, Feb 2009]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -8 ACMG points.
BA1
GnomAdExome4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.302 is higher than 0.05.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ACAT1 | ENST00000672284.1 | c.-199+4299_-199+4301delAAA | intron_variant | Intron 1 of 11 | ENSP00000500444.1 | |||||
ENSG00000255467 | ENST00000525548.1 | n.389+93_389+95delTTT | intron_variant | Intron 1 of 3 | 3 |
Frequencies
GnomAD3 genomes AF: 0.0102 AC: 1446AN: 141968Hom.: 19 Cov.: 0
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GnomAD4 exome AF: 0.201 AC: 21494AN: 107166Hom.: 2 AF XY: 0.203 AC XY: 11649AN XY: 57374
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GnomAD4 genome AF: 0.0102 AC: 1453AN: 142034Hom.: 19 Cov.: 0 AF XY: 0.0104 AC XY: 717AN XY: 68656
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Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at