13-30733158-CA-C

Variant names:

• chr13-30733158-CA-C
• rs34069656
• ENST00000617770.4:c.117-2392delA

Variant summary

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

The NM_001204406.2(ALOX5AP):​c.117-2375delA 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 0.33 (3022 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 = 0.456 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.117-2375delA		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.117-2392delA		intron	N/A	ENSP00000479870.1	A0A087WW23

Frequencies

GnomAD3 genomes AF: 0.331 AC: 27148 AN: 81924 Hom.: 3028 Cov.: 0

Gnomad AFR AF: 0.463

Gnomad AMI AF: 0.194

Gnomad AMR AF: 0.347

Gnomad ASJ AF: 0.268

Gnomad EAS AF: 0.283

Gnomad SAS AF: 0.447

Gnomad FIN AF: 0.143

Gnomad MID AF: 0.376

Gnomad NFE AF: 0.243

Gnomad OTH AF: 0.319

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

GnomAD4 genome AF: 0.331 AC: 27139 AN: 81936 Hom.: 3022 Cov.: 0 AF XY: 0.334 AC XY: 12883 AN XY: 38566

African (AFR) AF: 0.463 AC: 12218 AN: 26392

American (AMR) AF: 0.347 AC: 2920 AN: 8408

Ashkenazi Jewish (ASJ) AF: 0.268 AC: 532 AN: 1988

East Asian (EAS) AF: 0.283 AC: 801 AN: 2830

South Asian (SAS) AF: 0.445 AC: 1230 AN: 2766

European-Finnish (FIN) AF: 0.143 AC: 388 AN: 2708

Middle Eastern (MID) AF: 0.370 AC: 60 AN: 162

European-Non Finnish (NFE) AF: 0.243 AC: 8549 AN: 35138

Other (OTH) AF: 0.319 AC: 362 AN: 1136

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

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;