chr16-89093708-C-T
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The ENST00000537895.5(ACSF3):c.-130+5230C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0115 in 151,764 control chromosomes in the GnomAD database, including 26 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.011 ( 26 hom., cov: 33)
Exomes 𝑓: 0.0066 ( 0 hom. )
Consequence
ACSF3
ENST00000537895.5 intron
ENST00000537895.5 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.246
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 -14 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.77).
BP6
?
Variant 16-89093708-C-T is Benign according to our data. Variant chr16-89093708-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 1329720.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.0115 (1740/151312) while in subpopulation AFR AF= 0.0351 (1457/41468). AF 95% confidence interval is 0.0336. There are 26 homozygotes in gnomad4. There are 891 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd at 25 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ACSF3 | ENST00000537895.5 | c.-130+5230C>T | intron_variant | 4 |
Frequencies
GnomAD3 genomes ? AF: 0.0114 AC: 1721AN: 151210Hom.: 25 Cov.: 33
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GnomAD4 exome AF: 0.00664 AC: 3AN: 452Hom.: 0 AF XY: 0.00585 AC XY: 2AN XY: 342
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GnomAD4 genome ? AF: 0.0115 AC: 1740AN: 151312Hom.: 26 Cov.: 33 AF XY: 0.0121 AC XY: 891AN XY: 73898
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Jun 24, 2021 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at