rs11571364

chr17-7008372-G-A

Variant summary

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

The NM_000697.3(ALOX12):c.1541-1375G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0445 in 152,266 control chromosomes in the GnomAD database, including 212 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 0.045 (212 hom., cov: 32)
• Consequence: ALOX12 NM_000697.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.83

Genes affected

ALOX12 (HGNC:429): (arachidonate 12-lipoxygenase, 12S type) This gene encodes a member of the lipoxygenase family of proteins. The encoded enzyme acts on different polyunsaturated fatty acid substrates to generate bioactive lipid mediators including eicosanoids and lipoxins. The encoded enzyme and its reaction products have been shown to regulate platelet function. Elevated expression of this gene has been observed in pancreatic islets derived from human diabetes patients. Allelic variants in this gene may be associated with susceptibility to toxoplasmosis. Multiple pseudogenes of this gene have been identified in the human genome. [provided by RefSeq, Aug 2017]

ALOX12-AS1 (HGNC:51342): (ALOX12 antisense RNA 1)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0636 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ALOX12	NM_000697.3	c.1541-1375G>A		intron_variant		ENST00000251535.11
ALOX12-AS1	NR_040089.1	n.233+1424C>T		intron_variant, non_coding_transcript_variant
ALOX12	XM_011523780.3	c.1334-1375G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ALOX12	ENST00000251535.11	c.1541-1375G>A		intron_variant		1	NM_000697.3	P1
ALOX12-AS1	ENST00000653385.1	n.139+3824C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0446 AC: 6784 AN: 152148 Hom.: 212 Cov.: 32

Gnomad AFR AF: 0.0128

Gnomad AMI AF: 0.0208

Gnomad AMR AF: 0.0582

Gnomad ASJ AF: 0.0786

Gnomad EAS AF: 0.000576

Gnomad SAS AF: 0.0149

Gnomad FIN AF: 0.0380

Gnomad MID AF: 0.0918

Gnomad NFE AF: 0.0652

Gnomad OTH AF: 0.0608

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

GnomAD4 genome AF: 0.0445 AC: 6782 AN: 152266 Hom.: 212 Cov.: 32 AF XY: 0.0425 AC XY: 3165 AN XY: 74460

Gnomad4 AFR AF: 0.0127

Gnomad4 AMR AF: 0.0581

Gnomad4 ASJ AF: 0.0786

Gnomad4 EAS AF: 0.000578

Gnomad4 SAS AF: 0.0153

Gnomad4 FIN AF: 0.0380

Gnomad4 NFE AF: 0.0653

Gnomad4 OTH AF: 0.0601

Alfa AF: 0.0559 Hom.: 87

Bravo AF: 0.0459

Asia WGS AF: 0.0120 AC: 40 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
Cadd	Benign	11
Dann	Benign	0.61

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: rs11571364; hg19: chr17-6911691;