rs9506352

Positions:

• chr13-30746678-G-A

Variant summary

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

The NM_001629.4(ALOX5AP):​c.170+2519G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.233 in 152,172 control chromosomes in the GnomAD database, including 5,193 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 0.23 (5193 hom., cov: 33)
• Consequence: ALOX5AP NM_001629.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.321

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=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.312 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ALOX5AP	NM_001629.4	c.170+2519G>A		intron_variant		ENST00000380490.5	NP_001620.2
LOC124903146	XR_007063743.1	n.90-2039C>T		intron_variant, non_coding_transcript_variant
ALOX5AP	XM_017020522.3	c.-17G>A		5_prime_UTR_variant	2/5		XP_016876011.1
ALOX5AP	NM_001204406.2	c.341+2519G>A		intron_variant			NP_001191335.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ALOX5AP	ENST00000380490.5	c.170+2519G>A		intron_variant		1	NM_001629.4	ENSP00000369858	P1
ALOX5AP	ENST00000617770.4	c.341+2519G>A		intron_variant		1		ENSP00000479870

Frequencies

GnomAD3 genomes AF: 0.233 AC: 35439 AN: 152054 Hom.: 5199 Cov.: 33

Gnomad AFR AF: 0.0561

Gnomad AMI AF: 0.307

Gnomad AMR AF: 0.264

Gnomad ASJ AF: 0.257

Gnomad EAS AF: 0.247

Gnomad SAS AF: 0.250

Gnomad FIN AF: 0.324

Gnomad MID AF: 0.266

Gnomad NFE AF: 0.315

Gnomad OTH AF: 0.230

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

GnomAD4 genome AF: 0.233 AC: 35435 AN: 152172 Hom.: 5193 Cov.: 33 AF XY: 0.234 AC XY: 17382 AN XY: 74380

Gnomad4 AFR AF: 0.0560

Gnomad4 AMR AF: 0.264

Gnomad4 ASJ AF: 0.257

Gnomad4 EAS AF: 0.248

Gnomad4 SAS AF: 0.251

Gnomad4 FIN AF: 0.324

Gnomad4 NFE AF: 0.315

Gnomad4 OTH AF: 0.228

Alfa AF: 0.264 Hom.: 1146

Bravo AF: 0.221

Asia WGS AF: 0.199 AC: 690 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	0.37
DANN	Benign	0.77

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: rs9506352; hg19: chr13-31320815;