rs2228064
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Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1
The NM_000698.5(ALOX5):c.270G>A(p.Thr90=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0222 in 1,613,990 control chromosomes in the GnomAD database, including 3,665 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 0.091 ( 1862 hom., cov: 33)
Exomes 𝑓: 0.015 ( 1803 hom. )
Consequence
ALOX5
NM_000698.5 synonymous
NM_000698.5 synonymous
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -2.61
Genes affected
ALOX5 (HGNC:435): (arachidonate 5-lipoxygenase) This gene encodes a member of the lipoxygenase gene family and plays a dual role in the synthesis of leukotrienes from arachidonic acid. The encoded protein, which is expressed specifically in bone marrow-derived cells, catalyzes the conversion of arachidonic acid to 5(S)-hydroperoxy-6-trans-8,11,14-cis-eicosatetraenoic acid, and further to the allylic epoxide 5(S)-trans-7,9-trans-11,14-cis-eicosatetrenoic acid (leukotriene A4). Leukotrienes are important mediators of a number of inflammatory and allergic conditions. Mutations in the promoter region of this gene lead to a diminished response to antileukotriene drugs used in the treatment of asthma and may also be associated with atherosclerosis and several cancers. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jan 2012]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -13 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.6).
BP7
?
Synonymous conserved (PhyloP=-2.61 with no splicing effect.
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.286 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ALOX5 | NM_000698.5 | c.270G>A | p.Thr90= | synonymous_variant | 2/14 | ENST00000374391.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ALOX5 | ENST00000374391.7 | c.270G>A | p.Thr90= | synonymous_variant | 2/14 | 1 | NM_000698.5 | P1 | |
ALOX5 | ENST00000542434.5 | c.270G>A | p.Thr90= | synonymous_variant | 2/13 | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.0912 AC: 13870AN: 152086Hom.: 1860 Cov.: 33
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GnomAD3 exomes AF: 0.0362 AC: 9083AN: 251184Hom.: 797 AF XY: 0.0287 AC XY: 3904AN XY: 135820
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GnomAD4 exome AF: 0.0150 AC: 21935AN: 1461786Hom.: 1803 Cov.: 33 AF XY: 0.0138 AC XY: 10019AN XY: 727196
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GnomAD4 genome ? AF: 0.0913 AC: 13898AN: 152204Hom.: 1862 Cov.: 33 AF XY: 0.0880 AC XY: 6552AN XY: 74416
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Not reported inComputational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at