chr13-30729828-G-A

Variant names:

• chr13-30729828-G-A
• rs17216473
• ENST00000617770.4:c.117-5723G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001204406.2(ALOX5AP):​c.117-5723G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.152 in 152,060 control chromosomes in the GnomAD database, including 1,852 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 0.15 (1852 hom., cov: 32)
• Consequence: ALOX5AP NM_001204406.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.739
• Publications: 16 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]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.197 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001204406.2. 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_001204406.2		c.117-5723G>A		intron	N/A	NP_001191335.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ALOX5AP	ENST00000617770.4	TSL:1	c.117-5723G>A		intron	N/A	ENSP00000479870.1

Frequencies

GnomAD3 genomes AF: 0.152 AC: 23168 AN: 151942 Hom.: 1853 Cov.: 32

Gnomad AFR AF: 0.194

Gnomad AMI AF: 0.110

Gnomad AMR AF: 0.106

Gnomad ASJ AF: 0.147

Gnomad EAS AF: 0.186

Gnomad SAS AF: 0.210

Gnomad FIN AF: 0.142

Gnomad MID AF: 0.152

Gnomad NFE AF: 0.134

Gnomad OTH AF: 0.135

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

GnomAD4 genome AF: 0.152 AC: 23157 AN: 152060 Hom.: 1852 Cov.: 32 AF XY: 0.154 AC XY: 11474 AN XY: 74342

African (AFR) AF: 0.194 AC: 8033 AN: 41440

American (AMR) AF: 0.106 AC: 1618 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.147 AC: 511 AN: 3470

East Asian (EAS) AF: 0.186 AC: 961 AN: 5176

South Asian (SAS) AF: 0.208 AC: 1002 AN: 4814

European-Finnish (FIN) AF: 0.142 AC: 1495 AN: 10562

Middle Eastern (MID) AF: 0.153 AC: 45 AN: 294

European-Non Finnish (NFE) AF: 0.134 AC: 9111 AN: 67990

Other (OTH) AF: 0.133 AC: 281 AN: 2114

Alfa AF: 0.0667 Hom.: 78

Bravo AF: 0.149

Asia WGS AF: 0.185 AC: 645 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	4.4
DANN	Benign	0.68
PhyloP100		0.74

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs17216473; hg19: chr13-31303965;