rs9551960

chr13-30742803-G-Achr13-30742803-G-Cchr13-30742803-G-T

Variant summary

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

The NM_001629.4(ALOX5AP):c.71-1257G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.466 in 150,484 control chromosomes in the GnomAD database, including 18,826 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 0.47 (18826 hom., cov: 28)
• Consequence: ALOX5AP NM_001629.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.224

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 (EAS) allele frequency at 95% confidence interval = 0.63 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ALOX5AP	NM_001629.4	c.71-1257G>A		intron_variant		ENST00000380490.5
LOC124903146	XR_007063743.1	n.220+1706C>T		intron_variant, non_coding_transcript_variant
ALOX5AP	NM_001204406.2	c.242-1257G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ALOX5AP	ENST00000380490.5	c.71-1257G>A		intron_variant		1	NM_001629.4	P1
ALOX5AP	ENST00000617770.4	c.242-1257G>A		intron_variant		1
ALOX5AP	ENST00000479597.1	n.210+258G>A		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.466 AC: 70113 AN: 150366 Hom.: 18821 Cov.: 28

Gnomad AFR AF: 0.183

Gnomad AMI AF: 0.431

Gnomad AMR AF: 0.531

Gnomad ASJ AF: 0.555

Gnomad EAS AF: 0.648

Gnomad SAS AF: 0.580

Gnomad FIN AF: 0.567

Gnomad MID AF: 0.513

Gnomad NFE AF: 0.581

Gnomad OTH AF: 0.494

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

GnomAD4 genome AF: 0.466 AC: 70144 AN: 150484 Hom.: 18826 Cov.: 28 AF XY: 0.470 AC XY: 34453 AN XY: 73270

Gnomad4 AFR AF: 0.183

Gnomad4 AMR AF: 0.531

Gnomad4 ASJ AF: 0.555

Gnomad4 EAS AF: 0.649

Gnomad4 SAS AF: 0.582

Gnomad4 FIN AF: 0.567

Gnomad4 NFE AF: 0.581

Gnomad4 OTH AF: 0.497

Alfa AF: 0.447 Hom.: 2869

Bravo AF: 0.452

Asia WGS AF: 0.574 AC: 1995 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
Cadd	Benign	8.9
Dann	Benign	0.73

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: rs9551960; hg19: chr13-31316940;