rs17222814

Positions:

• chr13-30725416-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000617770.4(ALOX5AP):​c.117-10135G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0693 in 152,304 control chromosomes in the GnomAD database, including 480 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 0.069 (480 hom., cov: 34)
• Consequence: ALOX5AP ENST00000617770.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.285

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.102 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ALOX5AP	NM_001204406.2	c.117-10135G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ALOX5AP	ENST00000617770.4	c.117-10135G>A		intron_variant		1

Frequencies

GnomAD3 genomes AF: 0.0694 AC: 10560 AN: 152188 Hom.: 481 Cov.: 34

Gnomad AFR AF: 0.0181

Gnomad AMI AF: 0.0659

Gnomad AMR AF: 0.0509

Gnomad ASJ AF: 0.100

Gnomad EAS AF: 0.000385

Gnomad SAS AF: 0.0969

Gnomad FIN AF: 0.0876

Gnomad MID AF: 0.0601

Gnomad NFE AF: 0.104

Gnomad OTH AF: 0.0697

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

GnomAD4 genome AF: 0.0693 AC: 10561 AN: 152304 Hom.: 480 Cov.: 34 AF XY: 0.0697 AC XY: 5192 AN XY: 74464

Gnomad4 AFR AF: 0.0181

Gnomad4 AMR AF: 0.0509

Gnomad4 ASJ AF: 0.100

Gnomad4 EAS AF: 0.000386

Gnomad4 SAS AF: 0.0974

Gnomad4 FIN AF: 0.0876

Gnomad4 NFE AF: 0.104

Gnomad4 OTH AF: 0.0690

Alfa AF: 0.0947 Hom.: 715

Bravo AF: 0.0625

Asia WGS AF: 0.0320 AC: 113 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.3
DANN	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17222814; hg19: chr13-31299553;