rs9506352

Variant names:

• chr13-30746678-G-A
• rs9506352
• NM_001629.4:c.170+2519G>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 8 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 -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 rank	MANE	Protein	UniProt
ALOX5AP	NM_001629.4	c.170+2519G>A		intron_variant	Intron 2 of 4	ENST00000380490.5	NP_001620.2
ALOX5AP	XM_017020522.3	c.-17G>A		5_prime_UTR_variant	Exon 2 of 5		XP_016876011.1
ALOX5AP	NM_001204406.2	c.341+2519G>A		intron_variant	Intron 3 of 5		NP_001191335.1
LOC124903146	XR_007063743.1	n.90-2039C>T		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ALOX5AP	ENST00000380490.5	c.170+2519G>A		intron_variant	Intron 2 of 4	1	NM_001629.4	ENSP00000369858.3
ALOX5AP	ENST00000617770.4	c.341+2519G>A		intron_variant	Intron 3 of 5	1		ENSP00000479870.1

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

African (AFR) AF: 0.0560 AC: 2328 AN: 41566

American (AMR) AF: 0.264 AC: 4031 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.257 AC: 890 AN: 3464

East Asian (EAS) AF: 0.248 AC: 1284 AN: 5172

South Asian (SAS) AF: 0.251 AC: 1209 AN: 4820

European-Finnish (FIN) AF: 0.324 AC: 3419 AN: 10556

Middle Eastern (MID) AF: 0.245 AC: 72 AN: 294

European-Non Finnish (NFE) AF: 0.315 AC: 21441 AN: 67994

Other (OTH) AF: 0.228 AC: 481 AN: 2108

Alfa AF: 0.260 Hom.: 1152

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
PhyloP100		-0.32
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs9506352; hg19: chr13-31320815;