chr12-109166863-C-T
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 1P and 6B. PP2BP4_StrongBP6_Moderate
The NM_001093.4(ACACB):c.656C>T(p.Pro219Leu) variant causes a missense, splice region change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000211 in 1,613,882 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. 1/1 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_001093.4 missense, splice_region
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ACACB | NM_001093.4 | c.656C>T | p.Pro219Leu | missense_variant, splice_region_variant | 3/53 | ENST00000338432.12 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ACACB | ENST00000338432.12 | c.656C>T | p.Pro219Leu | missense_variant, splice_region_variant | 3/53 | 1 | NM_001093.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000198 AC: 30AN: 151898Hom.: 0 Cov.: 29
GnomAD3 exomes AF: 0.000486 AC: 122AN: 251184Hom.: 1 AF XY: 0.000405 AC XY: 55AN XY: 135780
GnomAD4 exome AF: 0.000212 AC: 310AN: 1461866Hom.: 2 Cov.: 31 AF XY: 0.000204 AC XY: 148AN XY: 727240
GnomAD4 genome ? AF: 0.000204 AC: 31AN: 152016Hom.: 0 Cov.: 29 AF XY: 0.000175 AC XY: 13AN XY: 74294
ClinVar
Submissions by phenotype
ACACB-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Jan 11, 2022 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at