13-30733158-CAAAAAAA-CAAAAAAAA

Variant names:

• chr13-30733158-C-CA
• rs34069656
• ENST00000617770.4:c.117-2393_117-2392insA

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BA1

The NM_001204406.2(ALOX5AP):​c.117-2375dupA variant causes a intron change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.067 (266 hom., cov: 0)
• Consequence: ALOX5AP NM_001204406.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.53
• Publications: 0 publications found

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]

LOC124903146 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.124 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001204406.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ALOX5AP	NM_001204406.2		c.117-2375dupA		intron	N/A	NP_001191335.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ALOX5AP	ENST00000617770.4	TSL:1	c.117-2393_117-2392insA		intron	N/A	ENSP00000479870.1

Frequencies

GnomAD3 genomes AF: 0.0672 AC: 5510 AN: 81956 Hom.: 266 Cov.: 0

Gnomad AFR AF: 0.128

Gnomad AMI AF: 0.0274

Gnomad AMR AF: 0.0860

Gnomad ASJ AF: 0.0120

Gnomad EAS AF: 0.116

Gnomad SAS AF: 0.0315

Gnomad FIN AF: 0.0396

Gnomad MID AF: 0.0529

Gnomad NFE AF: 0.0219

Gnomad OTH AF: 0.0628

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0673 AC: 5518 AN: 81968 Hom.: 266 Cov.: 0 AF XY: 0.0689 AC XY: 2654 AN XY: 38540

African (AFR) AF: 0.128 AC: 3391 AN: 26538

American (AMR) AF: 0.0863 AC: 726 AN: 8412

Ashkenazi Jewish (ASJ) AF: 0.0120 AC: 24 AN: 1998

East Asian (EAS) AF: 0.115 AC: 325 AN: 2822

South Asian (SAS) AF: 0.0317 AC: 88 AN: 2776

European-Finnish (FIN) AF: 0.0396 AC: 107 AN: 2704

Middle Eastern (MID) AF: 0.0494 AC: 8 AN: 162

European-Non Finnish (NFE) AF: 0.0219 AC: 767 AN: 35020

Other (OTH) AF: 0.0626 AC: 71 AN: 1134

Alfa AF: 0.00 Hom.: 0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		-1.5

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs34069656; hg19: chr13-31307295;