rs11571340

Positions:

• chr17-7004900-A-G

Variant summary

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

The NM_000697.3(ALOX12):​c.1162-357A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.106 in 152,224 control chromosomes in the GnomAD database, including 1,152 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 (1152 hom., cov: 31)
• Consequence: ALOX12 NM_000697.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.302

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=-0.92).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.252 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ALOX12	NM_000697.3	c.1162-357A>G		intron_variant		ENST00000251535.11	NP_000688.2
ALOX12-AS1	NR_040089.1	n.233+4896T>C		intron_variant, non_coding_transcript_variant
ALOX12	XM_011523780.3	c.955-357A>G		intron_variant			XP_011522082.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ALOX12	ENST00000251535.11	c.1162-357A>G		intron_variant		1	NM_000697.3	ENSP00000251535	P1
ALOX12-AS1	ENST00000653385.1	n.139+7296T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.106 AC: 16106 AN: 152106 Hom.: 1148 Cov.: 31

Gnomad AFR AF: 0.108

Gnomad AMI AF: 0.133

Gnomad AMR AF: 0.258

Gnomad ASJ AF: 0.0496

Gnomad EAS AF: 0.115

Gnomad SAS AF: 0.0414

Gnomad FIN AF: 0.151

Gnomad MID AF: 0.0318

Gnomad NFE AF: 0.0708

Gnomad OTH AF: 0.0931

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

GnomAD4 genome AF: 0.106 AC: 16126 AN: 152224 Hom.: 1152 Cov.: 31 AF XY: 0.111 AC XY: 8272 AN XY: 74440

Gnomad4 AFR AF: 0.108

Gnomad4 AMR AF: 0.259

Gnomad4 ASJ AF: 0.0496

Gnomad4 EAS AF: 0.114

Gnomad4 SAS AF: 0.0408

Gnomad4 FIN AF: 0.151

Gnomad4 NFE AF: 0.0707

Gnomad4 OTH AF: 0.0931

Alfa AF: 0.0791 Hom.: 1305

Bravo AF: 0.119

Asia WGS AF: 0.0920 AC: 319 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	3.3
DANN	Benign	0.63

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs11571340; hg19: chr17-6908219; COSMIC: COSV52349174; COSMIC: COSV52349174;