rs4075131

Positions:

• chr13-30736782-A-G

Variant summary

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

The NM_001629.4(ALOX5AP):​c.70+1107A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.297 in 152,112 control chromosomes in the GnomAD database, including 7,054 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 0.30 (7054 hom., cov: 33)
• Consequence: ALOX5AP NM_001629.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.252

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=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.376 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ALOX5AP	NM_001629.4	c.70+1107A>G		intron_variant		ENST00000380490.5	NP_001620.2
LOC124903146	XR_007063743.1	n.221-4045T>C		intron_variant, non_coding_transcript_variant
ALOX5AP	NM_001204406.2	c.241+1107A>G		intron_variant			NP_001191335.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ALOX5AP	ENST00000380490.5	c.70+1107A>G		intron_variant		1	NM_001629.4	ENSP00000369858	P1
ALOX5AP	ENST00000617770.4	c.241+1107A>G		intron_variant		1		ENSP00000479870

Frequencies

GnomAD3 genomes AF: 0.297 AC: 45130 AN: 151994 Hom.: 7043 Cov.: 33

Gnomad AFR AF: 0.381

Gnomad AMI AF: 0.476

Gnomad AMR AF: 0.326

Gnomad ASJ AF: 0.262

Gnomad EAS AF: 0.351

Gnomad SAS AF: 0.251

Gnomad FIN AF: 0.252

Gnomad MID AF: 0.285

Gnomad NFE AF: 0.245

Gnomad OTH AF: 0.291

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

GnomAD4 genome AF: 0.297 AC: 45163 AN: 152112 Hom.: 7054 Cov.: 33 AF XY: 0.298 AC XY: 22163 AN XY: 74342

Gnomad4 AFR AF: 0.381

Gnomad4 AMR AF: 0.327

Gnomad4 ASJ AF: 0.262

Gnomad4 EAS AF: 0.350

Gnomad4 SAS AF: 0.249

Gnomad4 FIN AF: 0.252

Gnomad4 NFE AF: 0.245

Gnomad4 OTH AF: 0.287

Alfa AF: 0.257 Hom.: 6922

Bravo AF: 0.310

Asia WGS AF: 0.301 AC: 1049 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.56
DANN	Benign	0.46

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: rs4075131; hg19: chr13-31310919;