rs4360791

Variant names:

• chr13-30743883-G-A
• rs4360791
• NM_001629.4:c.71-177G>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.71-177G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.499 in 151,924 control chromosomes in the GnomAD database, including 19,170 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 0.50 (19170 hom., cov: 31)
• Consequence: ALOX5AP NM_001629.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0340
• Publications: 7 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=-0.8).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.607 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001629.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ALOX5AP	NM_001629.4	MANE Select	c.71-177G>A		intron	N/A	NP_001620.2
	ALOX5AP	NM_001204406.2		c.242-177G>A		intron	N/A	NP_001191335.1	A0A087WW23

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ALOX5AP	ENST00000380490.5	TSL:1 MANE Select	c.71-177G>A		intron	N/A	ENSP00000369858.3	P20292
	ALOX5AP	ENST00000617770.4	TSL:1	c.242-177G>A		intron	N/A	ENSP00000479870.1	A0A087WW23
	ALOX5AP	ENST00000892335.1		c.71-177G>A		intron	N/A	ENSP00000562394.1

Frequencies

GnomAD3 genomes AF: 0.499 AC: 75679 AN: 151806 Hom.: 19158 Cov.: 31

Gnomad AFR AF: 0.567

Gnomad AMI AF: 0.359

Gnomad AMR AF: 0.500

Gnomad ASJ AF: 0.506

Gnomad EAS AF: 0.626

Gnomad SAS AF: 0.586

Gnomad FIN AF: 0.450

Gnomad MID AF: 0.475

Gnomad NFE AF: 0.450

Gnomad OTH AF: 0.504

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

GnomAD4 genome AF: 0.499 AC: 75746 AN: 151924 Hom.: 19170 Cov.: 31 AF XY: 0.502 AC XY: 37300 AN XY: 74246

African (AFR) AF: 0.567 AC: 23469 AN: 41404

American (AMR) AF: 0.500 AC: 7642 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.506 AC: 1756 AN: 3472

East Asian (EAS) AF: 0.625 AC: 3218 AN: 5146

South Asian (SAS) AF: 0.585 AC: 2820 AN: 4820

European-Finnish (FIN) AF: 0.450 AC: 4737 AN: 10534

Middle Eastern (MID) AF: 0.493 AC: 145 AN: 294

European-Non Finnish (NFE) AF: 0.450 AC: 30563 AN: 67960

Other (OTH) AF: 0.508 AC: 1071 AN: 2108

Alfa AF: 0.477 Hom.: 3164

Bravo AF: 0.506

Asia WGS AF: 0.625 AC: 2177 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	3.2
DANN	Benign	0.38
PhyloP100		-0.034
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: rs4360791; hg19: chr13-31318020;