13-30753703-G-T

Variant names:

• chr13-30753703-G-T
• rs9315048
• NM_001629.4:c.241+1581G>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001629.4(ALOX5AP):​c.241+1581G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.252 in 152,062 control chromosomes in the GnomAD database, including 4,919 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 0.25 (4919 hom., cov: 32)
• Consequence: ALOX5AP NM_001629.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.447
• Publications: 5 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=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.301 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ALOX5AP	NM_001629.4	MANE Select	c.241+1581G>T		intron	N/A	NP_001620.2
	ALOX5AP	NM_001204406.2		c.412+1581G>T		intron	N/A	NP_001191335.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ALOX5AP	ENST00000380490.5	TSL:1 MANE Select	c.241+1581G>T		intron	N/A	ENSP00000369858.3
	ALOX5AP	ENST00000617770.4	TSL:1	c.412+1581G>T		intron	N/A	ENSP00000479870.1

Frequencies

GnomAD3 genomes AF: 0.252 AC: 38263 AN: 151942 Hom.: 4919 Cov.: 32

Gnomad AFR AF: 0.306

Gnomad AMI AF: 0.238

Gnomad AMR AF: 0.234

Gnomad ASJ AF: 0.232

Gnomad EAS AF: 0.215

Gnomad SAS AF: 0.297

Gnomad FIN AF: 0.226

Gnomad MID AF: 0.229

Gnomad NFE AF: 0.228

Gnomad OTH AF: 0.244

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

GnomAD4 genome AF: 0.252 AC: 38277 AN: 152062 Hom.: 4919 Cov.: 32 AF XY: 0.253 AC XY: 18815 AN XY: 74312

African (AFR) AF: 0.305 AC: 12644 AN: 41462

American (AMR) AF: 0.235 AC: 3585 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.232 AC: 806 AN: 3472

East Asian (EAS) AF: 0.215 AC: 1112 AN: 5168

South Asian (SAS) AF: 0.296 AC: 1429 AN: 4820

European-Finnish (FIN) AF: 0.226 AC: 2383 AN: 10554

Middle Eastern (MID) AF: 0.228 AC: 67 AN: 294

European-Non Finnish (NFE) AF: 0.228 AC: 15519 AN: 67988

Other (OTH) AF: 0.243 AC: 515 AN: 2116

Alfa AF: 0.244 Hom.: 716

Bravo AF: 0.253

Asia WGS AF: 0.262 AC: 914 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.61
DANN	Benign	0.56
PhyloP100		-0.45
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: rs9315048; hg19: chr13-31327840;