13-30737959-A-T

Position:

• chr13-30737959-A-T

Variant summary

Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4 BA1

The NM_001629.4(ALOX5AP):​c.70+2284A>T variant causes a intron change. The variant allele was found at a frequency of 0.524 in 152,146 control chromosomes in the GnomAD database, including 24,104 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 0.52 (24104 hom., cov: 32)
• Consequence: ALOX5AP NM_001629.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.65

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 -9 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.18).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.67 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ALOX5AP	NM_001629.4	c.70+2284A>T		intron_variant		ENST00000380490.5
LOC124903146	XR_007063743.1	n.221-5222T>A		intron_variant, non_coding_transcript_variant
ALOX5AP	NM_001204406.2	c.241+2284A>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ALOX5AP	ENST00000380490.5	c.70+2284A>T		intron_variant		1	NM_001629.4	P1
ALOX5AP	ENST00000617770.4	c.241+2284A>T		intron_variant		1

Frequencies

GnomAD3 genomes AF: 0.524 AC: 79618 AN: 152028 Hom.: 24101 Cov.: 32

Gnomad AFR AF: 0.200

Gnomad AMI AF: 0.469

Gnomad AMR AF: 0.525

Gnomad ASJ AF: 0.622

Gnomad EAS AF: 0.611

Gnomad SAS AF: 0.594

Gnomad FIN AF: 0.704

Gnomad MID AF: 0.538

Gnomad NFE AF: 0.676

Gnomad OTH AF: 0.544

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

GnomAD4 genome AF: 0.524 AC: 79650 AN: 152146 Hom.: 24104 Cov.: 32 AF XY: 0.526 AC XY: 39101 AN XY: 74352

Gnomad4 AFR AF: 0.200

Gnomad4 AMR AF: 0.524

Gnomad4 ASJ AF: 0.622

Gnomad4 EAS AF: 0.611

Gnomad4 SAS AF: 0.595

Gnomad4 FIN AF: 0.704

Gnomad4 NFE AF: 0.676

Gnomad4 OTH AF: 0.547

Alfa AF: 0.591 Hom.: 3490

Bravo AF: 0.491

Asia WGS AF: 0.569 AC: 1979 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.18
CADD	Benign	18
DANN	Benign	0.88

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: rs10507391; hg19: chr13-31312096;