13-30733158-CAAAAAAA-CAAAAAAAA

Position:

• chr13-30733158-CAAAAAAA-CAAAAAAAA

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The NM_001204406.2(ALOX5AP):​c.117-2375dupA 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 0.067 (266 hom., cov: 0)
• Consequence: ALOX5AP NM_001204406.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.53

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 (AFR) allele frequency at 95% confidence interval = 0.124 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ALOX5AP	NM_001204406.2	c.117-2375dupA		intron_variant			NP_001191335.1
LOC124903146	XR_007063743.1	n.221-422dupT		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ALOX5AP	ENST00000617770.4	c.117-2375dupA		intron_variant		1		ENSP00000479870.1

Frequencies

GnomAD3 genomes AF: 0.0672 AC: 5510 AN: 81956 Hom.: 266 Cov.: 0

Gnomad AFR AF: 0.128

Gnomad AMI AF: 0.0274

Gnomad AMR AF: 0.0860

Gnomad ASJ AF: 0.0120

Gnomad EAS AF: 0.116

Gnomad SAS AF: 0.0315

Gnomad FIN AF: 0.0396

Gnomad MID AF: 0.0529

Gnomad NFE AF: 0.0219

Gnomad OTH AF: 0.0628

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

GnomAD4 genome AF: 0.0673 AC: 5518 AN: 81968 Hom.: 266 Cov.: 0 AF XY: 0.0689 AC XY: 2654 AN XY: 38540

Gnomad4 AFR AF: 0.128

Gnomad4 AMR AF: 0.0863

Gnomad4 ASJ AF: 0.0120

Gnomad4 EAS AF: 0.115

Gnomad4 SAS AF: 0.0317

Gnomad4 FIN AF: 0.0396

Gnomad4 NFE AF: 0.0219

Gnomad4 OTH AF: 0.0626

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: rs34069656; hg19: chr13-31307295;