rs10162089

chr13-30742601-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001629.4(ALOX5AP):c.71-1459G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.456 in 151,932 control chromosomes in the GnomAD database, including 16,042 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.46 (16040 hom., cov: 31)
  • Exomes 𝑓: 0.70 (2 hom.)
• Consequence: ALOX5AP NM_001629.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.917

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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.482 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ALOX5AP	NM_001629.4	c.71-1459G>A		intron_variant		ENST00000380490.5
LOC124903146	XR_007063743.1	n.220+1908C>T		intron_variant, non_coding_transcript_variant
ALOX5AP	NM_001204406.2	c.242-1459G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ALOX5AP	ENST00000380490.5	c.71-1459G>A		intron_variant		1	NM_001629.4	P1
ALOX5AP	ENST00000617770.4	c.242-1459G>A		intron_variant		1
ALOX5AP	ENST00000479597.1	n.210+56G>A		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.456 AC: 69219 AN: 151804 Hom.: 16035 Cov.: 31

Gnomad AFR AF: 0.488

Gnomad AMI AF: 0.356

Gnomad AMR AF: 0.370

Gnomad ASJ AF: 0.415

Gnomad EAS AF: 0.278

Gnomad SAS AF: 0.365

Gnomad FIN AF: 0.476

Gnomad MID AF: 0.373

Gnomad NFE AF: 0.477

Gnomad OTH AF: 0.436

GnomAD4 exome AF: 0.700 AC: 7 AN: 10 Hom.: 2 AF XY: 0.700 AC XY: 7 AN XY: 10

Gnomad4 NFE exome AF: 0.750

Gnomad4 OTH exome AF: 0.500

GnomAD4 genome AF: 0.456 AC: 69250 AN: 151922 Hom.: 16040 Cov.: 31 AF XY: 0.448 AC XY: 33227 AN XY: 74242

Gnomad4 AFR AF: 0.487

Gnomad4 AMR AF: 0.369

Gnomad4 ASJ AF: 0.415

Gnomad4 EAS AF: 0.279

Gnomad4 SAS AF: 0.366

Gnomad4 FIN AF: 0.476

Gnomad4 NFE AF: 0.477

Gnomad4 OTH AF: 0.433

Alfa AF: 0.454 Hom.: 15539

Bravo AF: 0.447

Asia WGS AF: 0.303 AC: 1052 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
Cadd	Benign	4.2
Dann	Benign	0.48

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs10162089; hg19: chr13-31316738;