13-30733158-CAAAAAAA-CAAAAAAAAAA

Variant names:

• chr13-30733158-C-CAAA
• rs34069656
• ENST00000617770.4:c.117-2393_117-2392insAAA

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BS2

The NM_001204406.2(ALOX5AP):​c.117-2377_117-2375dupAAA 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 0.0055 (6 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: Likely_benign. The variant received -4 ACMG points.

• BS2: High Homozygotes in GnomAd4 at 6 AR gene

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.117-2377_117-2375dupAAA		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.117-2393_117-2392insAAA		intron	N/A	ENSP00000479870.1	A0A087WW23

Frequencies

GnomAD3 genomes AF: 0.00548 AC: 451 AN: 82266 Hom.: 6 Cov.: 0

Gnomad AFR AF: 0.0162

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00154

Gnomad ASJ AF: 0.000499

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00107

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00

Gnomad OTH AF: 0.00264

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

GnomAD4 genome AF: 0.00547 AC: 450 AN: 82278 Hom.: 6 Cov.: 0 AF XY: 0.00566 AC XY: 219 AN XY: 38696

African (AFR) AF: 0.0163 AC: 432 AN: 26572

American (AMR) AF: 0.00154 AC: 13 AN: 8430

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

East Asian (EAS) AF: 0.00 AC: 0 AN: 2830

South Asian (SAS) AF: 0.000360 AC: 1 AN: 2780

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 2706

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 162

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 35242

Other (OTH) AF: 0.00263 AC: 3 AN: 1140

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;