NM_000019.4:c.-9T>A
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_000019.4(ACAT1):c.-9T>A variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.318 in 1,548,816 control chromosomes in the GnomAD database, including 83,240 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
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.-9T>A | 5_prime_UTR_variant | Exon 1 of 12 | ENST00000265838.9 | NP_000010.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.273 AC: 41578AN: 152116Hom.: 6932 Cov.: 34
GnomAD3 exomes AF: 0.361 AC: 54490AN: 150782Hom.: 10593 AF XY: 0.368 AC XY: 29661AN XY: 80608
GnomAD4 exome AF: 0.323 AC: 451699AN: 1396582Hom.: 76308 Cov.: 36 AF XY: 0.329 AC XY: 226982AN XY: 688990
GnomAD4 genome AF: 0.273 AC: 41580AN: 152234Hom.: 6932 Cov.: 34 AF XY: 0.282 AC XY: 20959AN XY: 74422
ClinVar
Submissions by phenotype
not specified Benign:3
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Deficiency of acetyl-CoA acetyltransferase Benign:3
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. -
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not provided Benign:2
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at