chr16-89094010-G-C
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_001243279.3(ACSF3):c.-194+14G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000247 in 169,920 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.00021 ( 0 hom., cov: 32)
Exomes 𝑓: 0.00052 ( 0 hom. )
Consequence
ACSF3
NM_001243279.3 intron
NM_001243279.3 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -3.26
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 Likely_benign. Variant got -4 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.91).
BP6
?
Variant 16-89094010-G-C is Benign according to our data. Variant chr16-89094010-G-C is described in ClinVar as [Likely_benign]. Clinvar id is 516974.Status of the report is criteria_provided_single_submitter, 1 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ACSF3 | NM_001243279.3 | c.-194+14G>C | intron_variant | ENST00000614302.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ACSF3 | ENST00000614302.5 | c.-194+14G>C | intron_variant | 5 | NM_001243279.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000215 AC: 32AN: 148666Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.000465 AC: 3AN: 6446Hom.: 0 AF XY: 0.000701 AC XY: 3AN XY: 4278
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GnomAD4 exome AF: 0.000520 AC: 11AN: 21148Hom.: 0 Cov.: 0 AF XY: 0.000683 AC XY: 10AN XY: 14650
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GnomAD4 genome ? AF: 0.000208 AC: 31AN: 148772Hom.: 0 Cov.: 32 AF XY: 0.000290 AC XY: 21AN XY: 72534
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Feb 06, 2018 | This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. - |
Computational scores
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Name
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BayesDel_noAF
Benign
Cadd
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Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at