rs11568070

Positions:

• chr17-4641943-G-A

Variant summary

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

The ENST00000570836.6(ALOX15):​c.-25-267C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0202 in 494,280 control chromosomes in the GnomAD database, including 188 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 0.020 (52 hom., cov: 31)
  • Exomes 𝑓: 0.020 (136 hom.)
• Consequence: ALOX15 ENST00000570836.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.264

Genes affected

ALOX15 (HGNC:433): (arachidonate 15-lipoxygenase) This gene encodes a member of the lipoxygenase family of proteins. The encoded enzyme acts on various polyunsaturated fatty acid substrates to generate various bioactive lipid mediators such as eicosanoids, hepoxilins, lipoxins, and other molecules. The encoded enzyme and its reaction products have been shown to regulate inflammation and immunity. Multiple pseudogenes of this gene have been identified in the human genome. [provided by RefSeq, Aug 2017]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAdExome4 highest subpopulation (MID) allele frequency at 95% confidence interval = 0.0624 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.4641943G>A		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ALOX15	ENST00000570836.6	c.-25-267C>T		intron_variant		2		ENSP00000458832.1
ALOX15	ENST00000574640.1	c.-292C>T		upstream_gene_variant		2		ENSP00000460483.1

Frequencies

GnomAD3 genomes AF: 0.0197 AC: 2996 AN: 152140 Hom.: 50 Cov.: 31

Gnomad AFR AF: 0.0240

Gnomad AMI AF: 0.00110

Gnomad AMR AF: 0.0226

Gnomad ASJ AF: 0.0778

Gnomad EAS AF: 0.000771

Gnomad SAS AF: 0.0336

Gnomad FIN AF: 0.00301

Gnomad MID AF: 0.0955

Gnomad NFE AF: 0.0162

Gnomad OTH AF: 0.0277

GnomAD4 exome AF: 0.0204 AC: 6988 AN: 342020 Hom.: 136 Cov.: 4 AF XY: 0.0217 AC XY: 3929 AN XY: 181160

Gnomad4 AFR exome AF: 0.0256

Gnomad4 AMR exome AF: 0.0177

Gnomad4 ASJ exome AF: 0.0802

Gnomad4 EAS exome AF: 0.000683

Gnomad4 SAS exome AF: 0.0350

Gnomad4 FIN exome AF: 0.00326

Gnomad4 NFE exome AF: 0.0169

Gnomad4 OTH exome AF: 0.0252

GnomAD4 genome AF: 0.0197 AC: 3002 AN: 152260 Hom.: 52 Cov.: 31 AF XY: 0.0193 AC XY: 1436 AN XY: 74460

Gnomad4 AFR AF: 0.0241

Gnomad4 AMR AF: 0.0225

Gnomad4 ASJ AF: 0.0778

Gnomad4 EAS AF: 0.000773

Gnomad4 SAS AF: 0.0332

Gnomad4 FIN AF: 0.00301

Gnomad4 NFE AF: 0.0162

Gnomad4 OTH AF: 0.0274

Alfa AF: 0.0209 Hom.: 4

Bravo AF: 0.0212

Asia WGS AF: 0.0270 AC: 95 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	2.0
DANN	Benign	0.64

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: rs11568070; hg19: chr17-4545238;