chr13-30733158-C-CAA

Variant names:

• chr13-30733158-C-CAA
• rs34069656
• ENST00000617770.4:c.117-2393_117-2392insAA

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BS1 BS2

The NM_001204406.2(ALOX5AP):​c.117-2376_117-2375dupAA 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 0.013 (16 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.

• BS1: Variant frequency is greater than expected in population afr. GnomAd4 allele frequency = 0.0133 (1091/82234) while in subpopulation AFR AF = 0.0376 (999/26560). AF 95% confidence interval is 0.0357. There are 16 homozygotes in GnomAd4. There are 508 alleles in the male GnomAd4 subpopulation. Median coverage is 0. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 16 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.117-2376_117-2375dupAA		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_117-2392insAA		intron	N/A	ENSP00000479870.1

Frequencies

GnomAD3 genomes AF: 0.0133 AC: 1091 AN: 82222 Hom.: 16 Cov.: 0

Gnomad AFR AF: 0.0377

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00534

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.000353

Gnomad SAS AF: 0.00107

Gnomad FIN AF: 0.000739

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000965

Gnomad OTH AF: 0.00616

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

GnomAD4 genome AF: 0.0133 AC: 1091 AN: 82234 Hom.: 16 Cov.: 0 AF XY: 0.0131 AC XY: 508 AN XY: 38670

African (AFR) AF: 0.0376 AC: 999 AN: 26560

American (AMR) AF: 0.00534 AC: 45 AN: 8430

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 2006

East Asian (EAS) AF: 0.000353 AC: 1 AN: 2832

South Asian (SAS) AF: 0.00108 AC: 3 AN: 2780

European-Finnish (FIN) AF: 0.000739 AC: 2 AN: 2706

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

European-Non Finnish (NFE) AF: 0.000966 AC: 34 AN: 35208

Other (OTH) AF: 0.00614 AC: 7 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;