rs9579646

Positions:

• chr13-30736442-G-A
• chr13-30736442-G-C
• chr13-30736442-G-T

Variant summary

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

The NM_001629.4(ALOX5AP):​c.70+767G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.469 in 151,748 control chromosomes in the GnomAD database, including 19,690 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 0.47 (19690 hom., cov: 32)
• Consequence: ALOX5AP NM_001629.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.309

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.768 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ALOX5AP	NM_001629.4	c.70+767G>A		intron_variant		ENST00000380490.5
LOC124903146	XR_007063743.1	n.221-3705C>T		intron_variant, non_coding_transcript_variant
ALOX5AP	NM_001204406.2	c.241+767G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ALOX5AP	ENST00000380490.5	c.70+767G>A		intron_variant		1	NM_001629.4	P1
ALOX5AP	ENST00000617770.4	c.241+767G>A		intron_variant		1

Frequencies

GnomAD3 genomes AF: 0.468 AC: 71006 AN: 151630 Hom.: 19655 Cov.: 32

Gnomad AFR AF: 0.775

Gnomad AMI AF: 0.506

Gnomad AMR AF: 0.477

Gnomad ASJ AF: 0.378

Gnomad EAS AF: 0.510

Gnomad SAS AF: 0.497

Gnomad FIN AF: 0.297

Gnomad MID AF: 0.424

Gnomad NFE AF: 0.306

Gnomad OTH AF: 0.439

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

GnomAD4 genome AF: 0.469 AC: 71100 AN: 151748 Hom.: 19690 Cov.: 32 AF XY: 0.470 AC XY: 34884 AN XY: 74188

Gnomad4 AFR AF: 0.775

Gnomad4 AMR AF: 0.478

Gnomad4 ASJ AF: 0.378

Gnomad4 EAS AF: 0.509

Gnomad4 SAS AF: 0.495

Gnomad4 FIN AF: 0.297

Gnomad4 NFE AF: 0.306

Gnomad4 OTH AF: 0.436

Alfa AF: 0.404 Hom.: 2401

Bravo AF: 0.499

Asia WGS AF: 0.560 AC: 1948 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	5.2
DANN	Benign	0.64

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs9579646; hg19: chr13-31310579;