13-30733158-CAAAAAAA-CAAAAAAAAA

Position:

• chr13-30733158-CAAAAAAA-CAAAAAAAAA

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BS1 BS2

The NM_001204406.2(ALOX5AP):​c.117-2376_117-2375dupAA 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 0.013 (16 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.

• BS1: Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.0133 (1091/82234) while in subpopulation AFR AF= 0.0376 (999/26560). AF 95% confidence interval is 0.0357. There are 16 homozygotes in gnomad4. There are 508 alleles in male gnomad4 subpopulation. Median coverage is 0. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 16 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ALOX5AP	NM_001204406.2	c.117-2376_117-2375dupAA		intron_variant			NP_001191335.1
LOC124903146	XR_007063743.1	n.221-423_221-422dupTT		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ALOX5AP	ENST00000617770.4	c.117-2376_117-2375dupAA		intron_variant		1		ENSP00000479870.1

Frequencies

GnomAD3 genomes AF: 0.0133 AC: 1091 AN: 82222 Hom.: 16 Cov.: 0

Gnomad AFR AF: 0.0377

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00534

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.000353

Gnomad SAS AF: 0.00107

Gnomad FIN AF: 0.000739

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000965

Gnomad OTH AF: 0.00616

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

GnomAD4 genome AF: 0.0133 AC: 1091 AN: 82234 Hom.: 16 Cov.: 0 AF XY: 0.0131 AC XY: 508 AN XY: 38670

Gnomad4 AFR AF: 0.0376

Gnomad4 AMR AF: 0.00534

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.000353

Gnomad4 SAS AF: 0.00108

Gnomad4 FIN AF: 0.000739

Gnomad4 NFE AF: 0.000966

Gnomad4 OTH AF: 0.00614

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;