rs11568131

chr17-4631313-G-A

Variant summary

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

The NM_001140.5(ALOX15):c.*287C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.117 in 444,254 control chromosomes in the GnomAD database, including 3,805 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 0.11 (1165 hom., cov: 32)
  • Exomes 𝑓: 0.12 (2640 hom.)
• Consequence: ALOX15 NM_001140.5 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.52

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.156 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ALOX15	NM_001140.5	c.*287C>T		3_prime_UTR_variant	14/14	ENST00000293761.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ALOX15	ENST00000293761.8	c.*287C>T		3_prime_UTR_variant	14/14	1	NM_001140.5	P1
ALOX15	ENST00000574640.1			downstream_gene_variant		2

Frequencies

GnomAD3 genomes AF: 0.110 AC: 16732 AN: 152162 Hom.: 1164 Cov.: 32

Gnomad AFR AF: 0.0303

Gnomad AMI AF: 0.194

Gnomad AMR AF: 0.144

Gnomad ASJ AF: 0.131

Gnomad EAS AF: 0.00173

Gnomad SAS AF: 0.0563

Gnomad FIN AF: 0.123

Gnomad MID AF: 0.171

Gnomad NFE AF: 0.158

Gnomad OTH AF: 0.129

GnomAD4 exome AF: 0.120 AC: 35093 AN: 291974 Hom.: 2640 Cov.: 2 AF XY: 0.119 AC XY: 17926 AN XY: 150760

Gnomad4 AFR exome AF: 0.0250

Gnomad4 AMR exome AF: 0.126

Gnomad4 ASJ exome AF: 0.126

Gnomad4 EAS exome AF: 0.000538

Gnomad4 SAS exome AF: 0.0556

Gnomad4 FIN exome AF: 0.115

Gnomad4 NFE exome AF: 0.147

Gnomad4 OTH exome AF: 0.123

GnomAD4 genome AF: 0.110 AC: 16736 AN: 152280 Hom.: 1165 Cov.: 32 AF XY: 0.108 AC XY: 8035 AN XY: 74450

Gnomad4 AFR AF: 0.0302

Gnomad4 AMR AF: 0.144

Gnomad4 ASJ AF: 0.131

Gnomad4 EAS AF: 0.00173

Gnomad4 SAS AF: 0.0561

Gnomad4 FIN AF: 0.123

Gnomad4 NFE AF: 0.158

Gnomad4 OTH AF: 0.128

Alfa AF: 0.142 Hom.: 564

Bravo AF: 0.108

Asia WGS AF: 0.0280 AC: 99 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
Cadd	Benign	0.11
Dann	Benign	0.28

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: rs11568131; hg19: chr17-4534608;