rs10507393
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001629.4(ALOX5AP):c.241+1262T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.233 in 152,178 control chromosomes in the GnomAD database, including 5,204 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 0.23 ( 5204 hom., cov: 33)
Consequence
ALOX5AP
NM_001629.4 intron
NM_001629.4 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.422
Genes affected
ALOX5AP (HGNC:436): (arachidonate 5-lipoxygenase activating protein) This gene encodes a protein which, with 5-lipoxygenase, is required for leukotriene synthesis. Leukotrienes are arachidonic acid metabolites which have been implicated in various types of inflammatory responses, including asthma, arthritis and psoriasis. This protein localizes to the plasma membrane. Inhibitors of its function impede translocation of 5-lipoxygenase from the cytoplasm to the cell membrane and inhibit 5-lipoxygenase activation. Alternatively spliced transcript variants encoding different isoforms have been identified for this gene. [provided by RefSeq, Feb 2011]
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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=-0.83).
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.312 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ALOX5AP | NM_001629.4 | c.241+1262T>C | intron_variant | ENST00000380490.5 | |||
LOC124903146 | XR_007063743.1 | n.89+2127A>G | intron_variant, non_coding_transcript_variant | ||||
ALOX5AP | NM_001204406.2 | c.412+1262T>C | intron_variant | ||||
ALOX5AP | XM_017020522.3 | c.121+1262T>C | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ALOX5AP | ENST00000380490.5 | c.241+1262T>C | intron_variant | 1 | NM_001629.4 | P1 | |||
ALOX5AP | ENST00000617770.4 | c.412+1262T>C | intron_variant | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.233 AC: 35495AN: 152058Hom.: 5210 Cov.: 33
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.233 AC: 35491AN: 152178Hom.: 5204 Cov.: 33 AF XY: 0.234 AC XY: 17418AN XY: 74382
GnomAD4 genome
?
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33
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17418
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74382
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697
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3478
ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
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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