rs5943427
Positions:
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong
The NM_001318510.2(ACSL4):c.-66+3029C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. 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 0.52 ( 11077 hom., 16863 hem., cov: 23)
Failed GnomAD Quality Control
Consequence
ACSL4
NM_001318510.2 intron
NM_001318510.2 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.154
Genes affected
ACSL4 (HGNC:3571): (acyl-CoA synthetase long chain family member 4) The protein encoded by this gene is an isozyme of the long-chain fatty-acid-coenzyme A ligase family. Although differing in substrate specificity, subcellular localization, and tissue distribution, all isozymes of this family convert free long-chain fatty acids into fatty acyl-CoA esters, and thereby play a key role in lipid biosynthesis and fatty acid degradation. This isozyme preferentially utilizes arachidonate as substrate. The absence of this enzyme may contribute to the cognitive disability or Alport syndrome. Alternative splicing of this gene generates multiple transcript variants. [provided by RefSeq, Jan 2016]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -4 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.95).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ACSL4 | NM_001318510.2 | c.-66+3029C>G | intron_variant | ENST00000672401.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ACSL4 | ENST00000672401.1 | c.-66+3029C>G | intron_variant | NM_001318510.2 | P4 |
Frequencies
GnomAD3 genomes ? AF: 0.520 AC: 57676AN: 110921Hom.: 11076 Cov.: 23 AF XY: 0.507 AC XY: 16826AN XY: 33155
GnomAD3 genomes
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23
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? Data not reliable, filtered out with message: InbreedingCoeff AF: 0.520 AC: 57710AN: 110974Hom.: 11077 Cov.: 23 AF XY: 0.508 AC XY: 16863AN XY: 33218
GnomAD4 genome
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Data not reliable, filtered out with message: InbreedingCoeff
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ClinVar
Not reported inComputational scores
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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