rs9579645

chr13-30736369-A-C

Variant summary

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

The NM_001629.4(ALOX5AP):c.70+694A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.22 in 152,026 control chromosomes in the GnomAD database, including 5,020 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 0.22 (5020 hom., cov: 32)
• Consequence: ALOX5AP NM_001629.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.117

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=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.418 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ALOX5AP	NM_001629.4	c.70+694A>C		intron_variant		ENST00000380490.5
LOC124903146	XR_007063743.1	n.221-3632T>G		intron_variant, non_coding_transcript_variant
ALOX5AP	NM_001204406.2	c.241+694A>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ALOX5AP	ENST00000380490.5	c.70+694A>C		intron_variant		1	NM_001629.4	P1
ALOX5AP	ENST00000617770.4	c.241+694A>C		intron_variant		1

Frequencies

GnomAD3 genomes AF: 0.219 AC: 33341 AN: 151910 Hom.: 5002 Cov.: 32

Gnomad AFR AF: 0.423

Gnomad AMI AF: 0.111

Gnomad AMR AF: 0.207

Gnomad ASJ AF: 0.200

Gnomad EAS AF: 0.159

Gnomad SAS AF: 0.285

Gnomad FIN AF: 0.0685

Gnomad MID AF: 0.242

Gnomad NFE AF: 0.125

Gnomad OTH AF: 0.212

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

GnomAD4 genome AF: 0.220 AC: 33400 AN: 152026 Hom.: 5020 Cov.: 32 AF XY: 0.218 AC XY: 16188 AN XY: 74332

Gnomad4 AFR AF: 0.423

Gnomad4 AMR AF: 0.207

Gnomad4 ASJ AF: 0.200

Gnomad4 EAS AF: 0.159

Gnomad4 SAS AF: 0.284

Gnomad4 FIN AF: 0.0685

Gnomad4 NFE AF: 0.125

Gnomad4 OTH AF: 0.213

Alfa AF: 0.152 Hom.: 2750

Bravo AF: 0.250

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
Cadd	Benign	1.8
Dann	Benign	0.42

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: rs9579645; hg19: chr13-31310506;