chr16-89100533-C-T
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_001243279.3(ACSF3):c.-20-129C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.69 in 892,160 control chromosomes in the GnomAD database, including 216,453 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.72 ( 39703 hom., cov: 33)
Exomes 𝑓: 0.68 ( 176750 hom. )
Consequence
ACSF3
NM_001243279.3 intron
NM_001243279.3 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -2.73
Genes affected
ACSF3 (HGNC:27288): (acyl-CoA synthetase family member 3) This gene encodes a member of the acyl-CoA synthetase family of enzymes that activate fatty acids by catalyzing the formation of a thioester linkage between fatty acids and coenzyme A. The encoded protein is localized to mitochondria, has high specificity for malonate and methylmalonate and possesses malonyl-CoA synthetase activity. Mutations in this gene are a cause of combined malonic and methylmalonic aciduria. Alternatively spliced transcript variants have been observed for this gene. [provided by RefSeq, Sep 2013]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -20 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.92).
BP6
?
Variant 16-89100533-C-T is Benign according to our data. Variant chr16-89100533-C-T is described in ClinVar as [Benign]. Clinvar id is 1188936.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.779 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ACSF3 | NM_001243279.3 | c.-20-129C>T | intron_variant | ENST00000614302.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ACSF3 | ENST00000614302.5 | c.-20-129C>T | intron_variant | 5 | NM_001243279.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.716 AC: 108906AN: 152018Hom.: 39682 Cov.: 33
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GnomAD4 exome AF: 0.685 AC: 506887AN: 740024Hom.: 176750 AF XY: 0.682 AC XY: 256652AN XY: 376336
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GnomAD4 genome ? AF: 0.716 AC: 108969AN: 152136Hom.: 39703 Cov.: 33 AF XY: 0.711 AC XY: 52915AN XY: 74382
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ClinVar
Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
Combined malonic and methylmalonic acidemia Benign:1
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Jul 14, 2021 | - - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jun 29, 2018 | - - |
Computational scores
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Cadd
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Benign
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at