rs6132784
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_032501.4(ACSS1):c.*611T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.164 in 1,320,066 control chromosomes in the GnomAD database, including 18,624 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 0.13 ( 1570 hom., cov: 33)
Exomes 𝑓: 0.17 ( 17054 hom. )
Consequence
ACSS1
NM_032501.4 3_prime_UTR
NM_032501.4 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.109
Genes affected
ACSS1 (HGNC:16091): (acyl-CoA synthetase short chain family member 1) This gene encodes a mitochondrial acetyl-CoA synthetase enzyme. A similar protein in mice plays an important role in the tricarboxylic acid cycle by catalyzing the conversion of acetate to acetyl CoA. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene. [provided by RefSeq, Nov 2011]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.86).
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.177 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ACSS1 | NM_032501.4 | c.*611T>C | 3_prime_UTR_variant | 14/14 | ENST00000323482.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ACSS1 | ENST00000323482.9 | c.*611T>C | 3_prime_UTR_variant | 14/14 | 1 | NM_032501.4 | P1 | ||
ACSS1 | ENST00000484396.1 | n.3848T>C | non_coding_transcript_exon_variant | 2/2 | 1 | ||||
ACSS1 | ENST00000537502.5 | c.*611T>C | 3_prime_UTR_variant | 13/13 | 2 | ||||
ACSS1 | ENST00000432802.6 | c.1663-226T>C | intron_variant | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.135 AC: 20508AN: 152140Hom.: 1572 Cov.: 33
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GnomAD4 exome AF: 0.168 AC: 196476AN: 1167808Hom.: 17054 Cov.: 32 AF XY: 0.167 AC XY: 93533AN XY: 558990
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GnomAD4 genome ? AF: 0.135 AC: 20506AN: 152258Hom.: 1570 Cov.: 33 AF XY: 0.130 AC XY: 9662AN XY: 74450
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3478
ClinVar
Not reported inComputational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at