chr13-30732492-C-G

Variant names:

• chr13-30732492-C-G
• rs11616333
• ENST00000617770.4:c.117-3059C>G

Variant summary

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

The ENST00000617770.4(ALOX5AP):​c.117-3059C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0354 in 152,312 control chromosomes in the GnomAD database, including 145 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 0.035 (145 hom., cov: 32)
• Consequence: ALOX5AP ENST00000617770.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.203
• Publications: 5 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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0512 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ALOX5AP	NM_001204406.2	c.117-3059C>G		intron_variant	Intron 1 of 5		NP_001191335.1
LOC124903146	XR_007063743.1	n.*30G>C		downstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ALOX5AP	ENST00000617770.4	c.117-3059C>G		intron_variant	Intron 1 of 5	1		ENSP00000479870.1

Frequencies

GnomAD3 genomes AF: 0.0354 AC: 5394 AN: 152194 Hom.: 145 Cov.: 32

Gnomad AFR AF: 0.00895

Gnomad AMI AF: 0.00877

Gnomad AMR AF: 0.0474

Gnomad ASJ AF: 0.0556

Gnomad EAS AF: 0.000385

Gnomad SAS AF: 0.0120

Gnomad FIN AF: 0.0305

Gnomad MID AF: 0.0854

Gnomad NFE AF: 0.0527

Gnomad OTH AF: 0.0488

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

GnomAD4 genome AF: 0.0354 AC: 5392 AN: 152312 Hom.: 145 Cov.: 32 AF XY: 0.0334 AC XY: 2490 AN XY: 74480

African (AFR) AF: 0.00893 AC: 371 AN: 41556

American (AMR) AF: 0.0474 AC: 725 AN: 15306

Ashkenazi Jewish (ASJ) AF: 0.0556 AC: 193 AN: 3472

East Asian (EAS) AF: 0.000386 AC: 2 AN: 5184

South Asian (SAS) AF: 0.0126 AC: 61 AN: 4828

European-Finnish (FIN) AF: 0.0305 AC: 324 AN: 10626

Middle Eastern (MID) AF: 0.0884 AC: 26 AN: 294

European-Non Finnish (NFE) AF: 0.0526 AC: 3581 AN: 68022

Other (OTH) AF: 0.0478 AC: 101 AN: 2112

Alfa AF: 0.0420 Hom.: 20

Bravo AF: 0.0364

Asia WGS AF: 0.00751 AC: 26 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.47
DANN	Benign	0.43
PhyloP100		-0.20

Splicing

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

Other links and lift over

dbSNP: rs11616333; hg19: chr13-31306629;