rs4073259

Variant names:

• chr13-30732134-G-A
• rs4073259
• ENST00000617770.4:c.117-3417G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000617770.4(ALOX5AP):​c.117-3417G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.497 in 152,190 control chromosomes in the GnomAD database, including 21,664 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.50 (21664 hom., cov: 33)
• Consequence: ALOX5AP ENST00000617770.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.520
• Publications: 17 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]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.643 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ALOX5AP	NM_001204406.2	c.117-3417G>A		intron_variant	Intron 1 of 5		NP_001191335.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ALOX5AP	ENST00000617770.4	c.117-3417G>A		intron_variant	Intron 1 of 5	1		ENSP00000479870.1

Frequencies

GnomAD3 genomes AF: 0.497 AC: 75655 AN: 152072 Hom.: 21663 Cov.: 33

Gnomad AFR AF: 0.200

Gnomad AMI AF: 0.458

Gnomad AMR AF: 0.489

Gnomad ASJ AF: 0.591

Gnomad EAS AF: 0.486

Gnomad SAS AF: 0.470

Gnomad FIN AF: 0.688

Gnomad MID AF: 0.525

Gnomad NFE AF: 0.648

Gnomad OTH AF: 0.525

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

GnomAD4 genome AF: 0.497 AC: 75678 AN: 152190 Hom.: 21664 Cov.: 33 AF XY: 0.497 AC XY: 37002 AN XY: 74408

African (AFR) AF: 0.200 AC: 8326 AN: 41530

American (AMR) AF: 0.488 AC: 7469 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.591 AC: 2052 AN: 3472

East Asian (EAS) AF: 0.486 AC: 2512 AN: 5168

South Asian (SAS) AF: 0.472 AC: 2279 AN: 4830

European-Finnish (FIN) AF: 0.688 AC: 7291 AN: 10590

Middle Eastern (MID) AF: 0.514 AC: 151 AN: 294

European-Non Finnish (NFE) AF: 0.648 AC: 44065 AN: 67986

Other (OTH) AF: 0.528 AC: 1115 AN: 2112

Alfa AF: 0.574 Hom.: 3394

Bravo AF: 0.466

Asia WGS AF: 0.419 AC: 1457 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	1.3
DANN	Benign	0.73
PhyloP100		-0.52

Splicing

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

Other links and lift over

dbSNP: rs4073259; hg19: chr13-31306271;