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. Variant got -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. 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

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

Verdict is Benign. Variant got -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.536 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ALOX5AP	NM_001629.4	c.242-1697_242-1696insAGAGAAAGCTGAAG		intron_variant	Intron 3 of 4	ENST00000380490.5	NP_001620.2
ALOX5AP	NM_001204406.2	c.413-1697_413-1696insAGAGAAAGCTGAAG		intron_variant	Intron 4 of 5		NP_001191335.1
ALOX5AP	XM_017020522.3	c.122-1697_122-1696insAGAGAAAGCTGAAG		intron_variant	Intron 3 of 4		XP_016876011.1
LOC124903146	XR_007063743.1	n.89+1265_89+1266insTCAGCTTTCTCTCT		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ALOX5AP	ENST00000380490.5	c.242-1699_242-1698insAGAGAGAAAGCTGA		intron_variant	Intron 3 of 4	1	NM_001629.4	ENSP00000369858.3
ALOX5AP	ENST00000617770.4	c.413-1699_413-1698insAGAGAGAAAGCTGA		intron_variant	Intron 4 of 5	1		ENSP00000479870.1

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

Gnomad4 AFR AF: 0.465

Gnomad4 AMR AF: 0.494

Gnomad4 ASJ AF: 0.494

Gnomad4 EAS AF: 0.375

Gnomad4 SAS AF: 0.413

Gnomad4 FIN AF: 0.555

Gnomad4 NFE AF: 0.540

Gnomad4 OTH AF: 0.491

Alfa AF: 0.521 Hom.: 2233

Asia WGS AF: 0.377 AC: 1309 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17238892; hg19: chr13-31328382;