13-30713844-G-A
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Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The ENST00000617770.4(ALOX5AP):c.116+3G>A variant causes a splice donor region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000981 in 650,680 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 Likely benign (★).
Frequency
Genomes: 𝑓 0.00012 ( 0 hom., cov: 24)
Exomes 𝑓: 0.0011 ( 0 hom. )
Consequence
ALOX5AP
ENST00000617770.4 splice_donor_region, intron
ENST00000617770.4 splice_donor_region, intron
Scores
2
Splicing: ADA: 0.00008935
2
Clinical Significance
Conservation
PhyloP100: 1.74
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 Likely_benign. Variant got -4 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.89).
BP6
Variant 13-30713844-G-A is Benign according to our data. Variant chr13-30713844-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 3041316.Status of the report is criteria_provided_single_submitter, 1 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ALOX5AP | NM_001204406.2 | c.116+3G>A | splice_donor_region_variant, intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ALOX5AP | ENST00000617770.4 | c.116+3G>A | splice_donor_region_variant, intron_variant | 1 |
Frequencies
GnomAD3 genomes AF: 0.000119 AC: 9AN: 75632Hom.: 0 Cov.: 24
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GnomAD3 exomes AF: 0.000545 AC: 59AN: 108216Hom.: 0 AF XY: 0.000553 AC XY: 33AN XY: 59672
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GnomAD4 exome AF: 0.00109 AC: 629AN: 575048Hom.: 0 Cov.: 33 AF XY: 0.00102 AC XY: 294AN XY: 287098
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GnomAD4 genome AF: 0.000119 AC: 9AN: 75632Hom.: 0 Cov.: 24 AF XY: 0.000136 AC XY: 5AN XY: 36740
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
ALOX5AP-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Jul 03, 2019 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational 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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dbscSNV1_ADA
Benign
dbscSNV1_RF
Benign
Find out detailed SpliceAI scores and Pangolin per-transcript scores at