13-30737959-A-T

Variant names:

• chr13-30737959-A-T
• rs10507391
• NM_001629.4:c.70+2284A>T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 62 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001629.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ALOX5AP	NM_001629.4	MANE Select	c.70+2284A>T		intron	N/A	NP_001620.2
	ALOX5AP	NM_001204406.2		c.241+2284A>T		intron	N/A	NP_001191335.1	A0A087WW23

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ALOX5AP	ENST00000380490.5	TSL:1 MANE Select	c.70+2284A>T		intron	N/A	ENSP00000369858.3	P20292
	ALOX5AP	ENST00000617770.4	TSL:1	c.241+2284A>T		intron	N/A	ENSP00000479870.1	A0A087WW23
	ALOX5AP	ENST00000892335.1		c.70+2284A>T		intron	N/A	ENSP00000562394.1

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

African (AFR) AF: 0.200 AC: 8322 AN: 41514

American (AMR) AF: 0.524 AC: 8018 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.622 AC: 2160 AN: 3470

East Asian (EAS) AF: 0.611 AC: 3165 AN: 5178

South Asian (SAS) AF: 0.595 AC: 2875 AN: 4830

European-Finnish (FIN) AF: 0.704 AC: 7437 AN: 10560

Middle Eastern (MID) AF: 0.537 AC: 158 AN: 294

European-Non Finnish (NFE) AF: 0.676 AC: 45931 AN: 67982

Other (OTH) AF: 0.547 AC: 1157 AN: 2114

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.18
CADD	Benign	18
DANN	Benign	0.88
PhyloP100		3.6
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs10507391; hg19: chr13-31312096;