13-30754245-G-GAGAGAGAAAGCTGA

Variant names:

• chr13-30754245-G-GAGAGAGAAAGCTGA
• rs17238892
• NM_001629.4:c.242-1697_242-1696insAGAGAAAGCTGAAG

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BA1

The NM_001629.4(ALOX5AP):​c.242-1697_242-1696insAGAGAAAGCTGAAG variant causes a intron change involving the alteration of a non-conserved nucleotide. It is difficult to determine the true allele frequency of this variant because it is of type INS_BIG, and the frequency of such variant types in population databases may be underestimated and unreliable. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.51 (19531 hom., cov: 0)
• Consequence: ALOX5AP NM_001629.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.521
• 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 -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.536 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.242-1697_242-1696insAGAGAAAGCTGAAG		intron	N/A	NP_001620.2
	ALOX5AP	NM_001204406.2		c.413-1697_413-1696insAGAGAAAGCTGAAG		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.242-1699_242-1698insAGAGAGAAAGCTGA		intron	N/A	ENSP00000369858.3	P20292
	ALOX5AP	ENST00000617770.4	TSL:1	c.413-1699_413-1698insAGAGAGAAAGCTGA		intron	N/A	ENSP00000479870.1	A0A087WW23
	ALOX5AP	ENST00000892335.1		c.242-1699_242-1698insAGAGAGAAAGCTGA		intron	N/A	ENSP00000562394.1

Frequencies

GnomAD3 genomes AF: 0.505 AC: 76616 AN: 151674 Hom.: 19525 Cov.: 0

Gnomad AFR AF: 0.465

Gnomad AMI AF: 0.641

Gnomad AMR AF: 0.494

Gnomad ASJ AF: 0.494

Gnomad EAS AF: 0.374

Gnomad SAS AF: 0.413

Gnomad FIN AF: 0.555

Gnomad MID AF: 0.415

Gnomad NFE AF: 0.540

Gnomad OTH AF: 0.495

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

GnomAD4 genome AF: 0.505 AC: 76660 AN: 151792 Hom.: 19531 Cov.: 0 AF XY: 0.500 AC XY: 37110 AN XY: 74192

African (AFR) AF: 0.465 AC: 19226 AN: 41366

American (AMR) AF: 0.494 AC: 7547 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.494 AC: 1705 AN: 3454

East Asian (EAS) AF: 0.375 AC: 1940 AN: 5176

South Asian (SAS) AF: 0.413 AC: 1991 AN: 4822

European-Finnish (FIN) AF: 0.555 AC: 5850 AN: 10534

Middle Eastern (MID) AF: 0.401 AC: 118 AN: 294

European-Non Finnish (NFE) AF: 0.540 AC: 36667 AN: 67872

Other (OTH) AF: 0.491 AC: 1035 AN: 2106

Alfa AF: 0.521 Hom.: 2233

Asia WGS AF: 0.377 AC: 1309 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		0.52
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs17238892; hg19: chr13-31328382;