13-30733158-CAA-C

Variant names:

• chr13-30733158-CAA-C
• rs34069656
• ENST00000617770.4:c.117-2392_117-2391delAA

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.

The NM_001204406.2(ALOX5AP):​c.117-2376_117-2375delAA 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 0.00062 (0 hom., cov: 0)
• Consequence: ALOX5AP NM_001204406.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.02
• 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: Uncertain_significance. The variant received 0 ACMG points.

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.117-2376_117-2375delAA		intron	N/A	NP_001191335.1	A0A087WW23

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ALOX5AP	ENST00000617770.4	TSL:1	c.117-2392_117-2391delAA		intron	N/A	ENSP00000479870.1	A0A087WW23

Frequencies

GnomAD3 genomes AF: 0.000620 AC: 51 AN: 82242 Hom.: 0 Cov.: 0

Gnomad AFR AF: 0.00113

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000713

Gnomad ASJ AF: 0.000499

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000716

Gnomad FIN AF: 0.00148

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000227

Gnomad OTH AF: 0.00

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

GnomAD4 genome AF: 0.000620 AC: 51 AN: 82254 Hom.: 0 Cov.: 0 AF XY: 0.000672 AC XY: 26 AN XY: 38690

African (AFR) AF: 0.00113 AC: 30 AN: 26578

American (AMR) AF: 0.000712 AC: 6 AN: 8422

Ashkenazi Jewish (ASJ) AF: 0.000499 AC: 1 AN: 2006

East Asian (EAS) AF: 0.00 AC: 0 AN: 2832

South Asian (SAS) AF: 0.000719 AC: 2 AN: 2780

European-Finnish (FIN) AF: 0.00148 AC: 4 AN: 2694

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 160

European-Non Finnish (NFE) AF: 0.000227 AC: 8 AN: 35234

Other (OTH) AF: 0.00 AC: 0 AN: 1138

Alfa AF: 0.00 Hom.: 0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		1.0

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs34069656; hg19: chr13-31307295;