chr10-45440444-G-A
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_StrongBP7BS2
The NM_000698.5(ALOX5):c.996G>A(p.Pro332=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000195 in 1,614,138 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 not provided (no stars).
Frequency
Genomes: 𝑓 0.00095 ( 0 hom., cov: 33)
Exomes 𝑓: 0.00012 ( 0 hom. )
Consequence
ALOX5
NM_000698.5 synonymous
NM_000698.5 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.451
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 -9 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.51).
BP7
?
Synonymous conserved (PhyloP=-0.451 with no splicing effect.
BS2
?
High AC in GnomAd at 143 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ALOX5 | NM_000698.5 | c.996G>A | p.Pro332= | synonymous_variant | 8/14 | ENST00000374391.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ALOX5 | ENST00000374391.7 | c.996G>A | p.Pro332= | synonymous_variant | 8/14 | 1 | NM_000698.5 | P1 | |
ALOX5 | ENST00000542434.5 | c.996G>A | p.Pro332= | synonymous_variant | 8/13 | 1 | |||
ALOX5 | ENST00000475300.1 | n.15G>A | non_coding_transcript_exon_variant | 1/2 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.000940 AC: 143AN: 152162Hom.: 0 Cov.: 33
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GnomAD3 exomes AF: 0.000298 AC: 75AN: 251364Hom.: 0 AF XY: 0.000302 AC XY: 41AN XY: 135866
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GnomAD4 exome AF: 0.000116 AC: 170AN: 1461858Hom.: 0 Cov.: 32 AF XY: 0.000131 AC XY: 95AN XY: 727234
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GnomAD4 genome ? AF: 0.000946 AC: 144AN: 152280Hom.: 0 Cov.: 33 AF XY: 0.000913 AC XY: 68AN XY: 74452
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ClinVar
Significance: not provided
Submissions summary: Other:1
Revision: no classification provided
LINK: link
Submissions by phenotype
not provided Other:1
not provided, no classification provided | literature only | Functional Genomics, Thrombosis Research Institute, India | - | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
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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