chr13-30733158-CA-C

Position:

• chr13-30733158-CA-C

Variant summary

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

The XR_007063743.1(LOC124903146):​n.221-422del variant causes a intron, non coding transcript 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 0.33 (3022 hom., cov: 0)
• Consequence: LOC124903146 XR_007063743.1 intron, non_coding_transcript
• 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 = 0.456 is higher than 0.05.

Transcripts

RefSeq

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

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.331 AC: 27148 AN: 81924 Hom.: 3028 Cov.: 0

Gnomad AFR AF: 0.463

Gnomad AMI AF: 0.194

Gnomad AMR AF: 0.347

Gnomad ASJ AF: 0.268

Gnomad EAS AF: 0.283

Gnomad SAS AF: 0.447

Gnomad FIN AF: 0.143

Gnomad MID AF: 0.376

Gnomad NFE AF: 0.243

Gnomad OTH AF: 0.319

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

GnomAD4 genome AF: 0.331 AC: 27139 AN: 81936 Hom.: 3022 Cov.: 0 AF XY: 0.334 AC XY: 12883 AN XY: 38566

Gnomad4 AFR AF: 0.463

Gnomad4 AMR AF: 0.347

Gnomad4 ASJ AF: 0.268

Gnomad4 EAS AF: 0.283

Gnomad4 SAS AF: 0.445

Gnomad4 FIN AF: 0.143

Gnomad4 NFE AF: 0.243

Gnomad4 OTH AF: 0.319

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;