11-108121592-C-G
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_000019.4(ACAT1):c.-15C>G variant causes a 5 prime UTR premature start codon gain change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0038 in 1,550,244 control chromosomes in the GnomAD database, including 197 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_000019.4 5_prime_UTR_premature_start_codon_gain
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ACAT1 | NM_000019.4 | c.-15C>G | 5_prime_UTR_premature_start_codon_gain_variant | Exon 1 of 12 | ENST00000265838.9 | NP_000010.1 | ||
ACAT1 | NM_000019.4 | c.-15C>G | 5_prime_UTR_variant | Exon 1 of 12 | ENST00000265838.9 | NP_000010.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ACAT1 | ENST00000265838 | c.-15C>G | 5_prime_UTR_premature_start_codon_gain_variant | Exon 1 of 12 | 1 | NM_000019.4 | ENSP00000265838.4 | |||
ACAT1 | ENST00000265838 | c.-15C>G | 5_prime_UTR_variant | Exon 1 of 12 | 1 | NM_000019.4 | ENSP00000265838.4 |
Frequencies
GnomAD3 genomes AF: 0.0204 AC: 3101AN: 152234Hom.: 107 Cov.: 34
GnomAD3 exomes AF: 0.00462 AC: 697AN: 150906Hom.: 20 AF XY: 0.00328 AC XY: 264AN XY: 80602
GnomAD4 exome AF: 0.00199 AC: 2783AN: 1397892Hom.: 91 Cov.: 30 AF XY: 0.00167 AC XY: 1149AN XY: 689580
GnomAD4 genome AF: 0.0204 AC: 3102AN: 152352Hom.: 106 Cov.: 34 AF XY: 0.0193 AC XY: 1439AN XY: 74498
ClinVar
Submissions by phenotype
Deficiency of acetyl-CoA acetyltransferase Benign:2
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This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. -
not specified Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at