13-30749205-A-G

Variant names:

• chr13-30749205-A-G
• rs4075692
• NM_001629.4:c.171-2847A>G

Variant summary

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

The NM_001629.4(ALOX5AP):​c.171-2847A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.581 in 152,076 control chromosomes in the GnomAD database, including 26,047 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 0.58 (26047 hom., cov: 32)
• Consequence: ALOX5AP NM_001629.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.587
• 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=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.713 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ALOX5AP	NM_001629.4	c.171-2847A>G		intron_variant	Intron 2 of 4	ENST00000380490.5	NP_001620.2
ALOX5AP	NM_001204406.2	c.342-2847A>G		intron_variant	Intron 3 of 5		NP_001191335.1
ALOX5AP	XM_017020522.3	c.50+2461A>G		intron_variant	Intron 2 of 4		XP_016876011.1
LOC124903146	XR_007063743.1	n.90-4566T>C		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ALOX5AP	ENST00000380490.5	c.171-2847A>G		intron_variant	Intron 2 of 4	1	NM_001629.4	ENSP00000369858.3
ALOX5AP	ENST00000617770.4	c.342-2847A>G		intron_variant	Intron 3 of 5	1		ENSP00000479870.1

Frequencies

GnomAD3 genomes AF: 0.581 AC: 88303 AN: 151958 Hom.: 26033 Cov.: 32

Gnomad AFR AF: 0.650

Gnomad AMI AF: 0.646

Gnomad AMR AF: 0.613

Gnomad ASJ AF: 0.566

Gnomad EAS AF: 0.733

Gnomad SAS AF: 0.612

Gnomad FIN AF: 0.541

Gnomad MID AF: 0.547

Gnomad NFE AF: 0.524

Gnomad OTH AF: 0.585

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

GnomAD4 genome AF: 0.581 AC: 88382 AN: 152076 Hom.: 26047 Cov.: 32 AF XY: 0.587 AC XY: 43616 AN XY: 74340

African (AFR) AF: 0.650 AC: 26970 AN: 41498

American (AMR) AF: 0.613 AC: 9377 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.566 AC: 1964 AN: 3468

East Asian (EAS) AF: 0.732 AC: 3788 AN: 5172

South Asian (SAS) AF: 0.612 AC: 2940 AN: 4806

European-Finnish (FIN) AF: 0.541 AC: 5711 AN: 10552

Middle Eastern (MID) AF: 0.561 AC: 165 AN: 294

European-Non Finnish (NFE) AF: 0.524 AC: 35636 AN: 67970

Other (OTH) AF: 0.589 AC: 1243 AN: 2112

Alfa AF: 0.549 Hom.: 30092

Bravo AF: 0.593

Asia WGS AF: 0.705 AC: 2454 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.5
DANN	Benign	0.38
PhyloP100		0.59
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: rs4075692; hg19: chr13-31323342;