chr13-30734192-T-G

Position:

• chr13-30734192-T-G

Variant summary

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

The ENST00000617770.4(ALOX5AP):​c.117-1359T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.145 in 152,220 control chromosomes in the GnomAD database, including 1,626 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 0.14 (1626 hom., cov: 32)
• Consequence: ALOX5AP ENST00000617770.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.128

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=-0.8).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.208 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC124903146	XR_007063743.1	n.221-1455A>C		intron_variant, non_coding_transcript_variant
ALOX5AP	NM_001204406.2	c.117-1359T>G		intron_variant			NP_001191335.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ALOX5AP	ENST00000617770.4	c.117-1359T>G		intron_variant		1		ENSP00000479870

Frequencies

GnomAD3 genomes AF: 0.145 AC: 22062 AN: 152102 Hom.: 1628 Cov.: 32

Gnomad AFR AF: 0.127

Gnomad AMI AF: 0.138

Gnomad AMR AF: 0.112

Gnomad ASJ AF: 0.154

Gnomad EAS AF: 0.187

Gnomad SAS AF: 0.220

Gnomad FIN AF: 0.157

Gnomad MID AF: 0.152

Gnomad NFE AF: 0.153

Gnomad OTH AF: 0.138

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

GnomAD4 genome AF: 0.145 AC: 22048 AN: 152220 Hom.: 1626 Cov.: 32 AF XY: 0.147 AC XY: 10948 AN XY: 74418

Gnomad4 AFR AF: 0.127

Gnomad4 AMR AF: 0.112

Gnomad4 ASJ AF: 0.154

Gnomad4 EAS AF: 0.187

Gnomad4 SAS AF: 0.219

Gnomad4 FIN AF: 0.157

Gnomad4 NFE AF: 0.153

Gnomad4 OTH AF: 0.136

Alfa AF: 0.140 Hom.: 1622

Bravo AF: 0.139

Asia WGS AF: 0.186 AC: 649 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	1.6
DANN	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17222919; hg19: chr13-31308329;