13-30738041-A-T

Position:

• chr13-30738041-A-T

Variant summary

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

The NM_001629.4(ALOX5AP):​c.70+2366A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.246 in 151,990 control chromosomes in the GnomAD database, including 4,763 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 0.25 (4763 hom., cov: 32)
• Consequence: ALOX5AP NM_001629.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.29

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=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.333 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ALOX5AP	NM_001629.4	c.70+2366A>T		intron_variant		ENST00000380490.5
LOC124903146	XR_007063743.1	n.221-5304T>A		intron_variant, non_coding_transcript_variant
ALOX5AP	NM_001204406.2	c.241+2366A>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ALOX5AP	ENST00000380490.5	c.70+2366A>T		intron_variant		1	NM_001629.4	P1
ALOX5AP	ENST00000617770.4	c.241+2366A>T		intron_variant		1

Frequencies

GnomAD3 genomes AF: 0.246 AC: 37415 AN: 151872 Hom.: 4757 Cov.: 32

Gnomad AFR AF: 0.198

Gnomad AMI AF: 0.433

Gnomad AMR AF: 0.293

Gnomad ASJ AF: 0.237

Gnomad EAS AF: 0.347

Gnomad SAS AF: 0.286

Gnomad FIN AF: 0.255

Gnomad MID AF: 0.222

Gnomad NFE AF: 0.252

Gnomad OTH AF: 0.243

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

GnomAD4 genome AF: 0.246 AC: 37426 AN: 151990 Hom.: 4763 Cov.: 32 AF XY: 0.251 AC XY: 18622 AN XY: 74292

Gnomad4 AFR AF: 0.198

Gnomad4 AMR AF: 0.294

Gnomad4 ASJ AF: 0.237

Gnomad4 EAS AF: 0.346

Gnomad4 SAS AF: 0.285

Gnomad4 FIN AF: 0.255

Gnomad4 NFE AF: 0.252

Gnomad4 OTH AF: 0.242

Alfa AF: 0.234 Hom.: 598

Bravo AF: 0.249

Asia WGS AF: 0.310 AC: 1079 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.8
DANN	Benign	0.69

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: rs12429692; hg19: chr13-31312178;