rs11078527
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001140.5(ALOX15):c.808-94C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.138 in 1,389,162 control chromosomes in the GnomAD database, including 14,827 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 0.11 ( 1125 hom., cov: 32)
Exomes 𝑓: 0.14 ( 13702 hom. )
Consequence
ALOX15
NM_001140.5 intron
NM_001140.5 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.709
Genes affected
ALOX15 (HGNC:433): (arachidonate 15-lipoxygenase) This gene encodes a member of the lipoxygenase family of proteins. The encoded enzyme acts on various polyunsaturated fatty acid substrates to generate various bioactive lipid mediators such as eicosanoids, hepoxilins, lipoxins, and other molecules. The encoded enzyme and its reaction products have been shown to regulate inflammation and immunity. Multiple pseudogenes of this gene have been identified in the human genome. [provided by RefSeq, Aug 2017]
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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=-0.87).
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.155 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ALOX15 | NM_001140.5 | c.808-94C>T | intron_variant | ENST00000293761.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ALOX15 | ENST00000293761.8 | c.808-94C>T | intron_variant | 1 | NM_001140.5 | P1 | |||
ALOX15 | ENST00000570836.6 | c.808-94C>T | intron_variant | 2 | P1 | ||||
ALOX15 | ENST00000574640.1 | c.691-94C>T | intron_variant | 2 | |||||
ALOX15 | ENST00000576572.1 | n.399-94C>T | intron_variant, non_coding_transcript_variant | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.109 AC: 16520AN: 152058Hom.: 1124 Cov.: 32
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GnomAD4 exome AF: 0.142 AC: 175329AN: 1236986Hom.: 13702 AF XY: 0.140 AC XY: 84723AN XY: 605274
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GnomAD4 genome ? AF: 0.109 AC: 16525AN: 152176Hom.: 1125 Cov.: 32 AF XY: 0.106 AC XY: 7893AN XY: 74400
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ClinVar
Not reported inComputational scores
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Name
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Prediction
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