rs9315051

chr13-30762040-A-G

Variant summary

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

The NM_001629.4(ALOX5AP):c.324-1904A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.11 in 152,216 control chromosomes in the GnomAD database, including 1,297 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 0.11 (1297 hom., cov: 32)
• Consequence: ALOX5AP NM_001629.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.750

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=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.213 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ALOX5AP	NM_001629.4	c.324-1904A>G		intron_variant		ENST00000380490.5
ALOX5AP	NM_001204406.2	c.495-1904A>G		intron_variant
ALOX5AP	XM_017020522.3	c.204-1904A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ALOX5AP	ENST00000380490.5	c.324-1904A>G		intron_variant		1	NM_001629.4	P1
ALOX5AP	ENST00000617770.4	c.495-1904A>G		intron_variant		1

Frequencies

GnomAD3 genomes AF: 0.110 AC: 16789 AN: 152098 Hom.: 1292 Cov.: 32

Gnomad AFR AF: 0.217

Gnomad AMI AF: 0.106

Gnomad AMR AF: 0.0792

Gnomad ASJ AF: 0.107

Gnomad EAS AF: 0.0179

Gnomad SAS AF: 0.115

Gnomad FIN AF: 0.0688

Gnomad MID AF: 0.104

Gnomad NFE AF: 0.0659

Gnomad OTH AF: 0.113

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

GnomAD4 genome AF: 0.110 AC: 16815 AN: 152216 Hom.: 1297 Cov.: 32 AF XY: 0.109 AC XY: 8111 AN XY: 74428

Gnomad4 AFR AF: 0.217

Gnomad4 AMR AF: 0.0790

Gnomad4 ASJ AF: 0.107

Gnomad4 EAS AF: 0.0179

Gnomad4 SAS AF: 0.115

Gnomad4 FIN AF: 0.0688

Gnomad4 NFE AF: 0.0659

Gnomad4 OTH AF: 0.112

Alfa AF: 0.0821 Hom.: 314

Bravo AF: 0.117

Asia WGS AF: 0.0830 AC: 288 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	0.28
Dann	Benign	0.70

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: rs9315051; hg19: chr13-31336177;