chr12-109167925-C-T
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1
The NM_001093.4(ACACB):c.816C>T(p.Ala272=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.204 in 1,613,306 control chromosomes in the GnomAD database, including 36,864 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 0.18 ( 3042 hom., cov: 28)
Exomes 𝑓: 0.21 ( 33822 hom. )
Consequence
ACACB
NM_001093.4 synonymous
NM_001093.4 synonymous
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -2.89
Genes affected
ACACB (HGNC:85): (acetyl-CoA carboxylase beta) Acetyl-CoA carboxylase (ACC) is a complex multifunctional enzyme system. ACC is a biotin-containing enzyme which catalyzes the carboxylation of acetyl-CoA to malonyl-CoA, the rate-limiting step in fatty acid synthesis. ACC-beta is thought to control fatty acid oxidation by means of the ability of malonyl-CoA to inhibit carnitine-palmitoyl-CoA transferase I, the rate-limiting step in fatty acid uptake and oxidation by mitochondria. ACC-beta may be involved in the regulation of fatty acid oxidation, rather than fatty acid biosynthesis. [provided by RefSeq, Oct 2022]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -13 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.71).
BP7
?
Synonymous conserved (PhyloP=-2.89 with no splicing effect.
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.513 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ACACB | NM_001093.4 | c.816C>T | p.Ala272= | synonymous_variant | 4/53 | ENST00000338432.12 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ACACB | ENST00000338432.12 | c.816C>T | p.Ala272= | synonymous_variant | 4/53 | 1 | NM_001093.4 | P1 | |
ACACB | ENST00000377848.7 | c.816C>T | p.Ala272= | synonymous_variant | 3/52 | 1 | P1 | ||
ACACB | ENST00000544726.2 | c.210C>T | p.Ala70= | synonymous_variant | 3/5 | 3 | |||
ACACB | ENST00000377854.9 | c.-3187C>T | 5_prime_UTR_variant | 3/47 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.179 AC: 27191AN: 151610Hom.: 3039 Cov.: 28
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GnomAD3 exomes AF: 0.233 AC: 58490AN: 251142Hom.: 8215 AF XY: 0.233 AC XY: 31571AN XY: 135746
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GnomAD4 exome AF: 0.206 AC: 301470AN: 1461578Hom.: 33822 Cov.: 34 AF XY: 0.208 AC XY: 150888AN XY: 727082
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GnomAD4 genome ? AF: 0.179 AC: 27204AN: 151728Hom.: 3042 Cov.: 28 AF XY: 0.184 AC XY: 13634AN XY: 74096
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Not reported inComputational scores
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Name
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at