Variant 17-6996757-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_000697.3(ALOX12):c.136-69G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.264 in 1,517,478 control chromosomes in the GnomAD database, including 56,706 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.20 ( 3917 hom., cov: 33)

Exomes 𝑓: 0.27 ( 52789 hom. )

Consequence

ALOX12
NM_000697.3 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -1.93

Variant links:

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 links:

ALOX12-AS1 (HGNC:):

ALOX12-AS1 links:

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

ALOX12-AS1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.89).

BP6

Variant 17-6996757-G-A is Benign according to our data. Variant chr17-6996757-G-A is described in ClinVar as [Benign]. Clinvar id is 1220801.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.313 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	MANE	Protein	UniProt
ALOX12	NM_000697.3 linkuse as main transcript	c.136-69G>A	intron_variant	ENST00000251535.11	NP_000688.2	P18054
ALOX12	XM_011523780.3 linkuse as main transcript	c.136-69G>A	intron_variant		XP_011522082.2
ALOX12-AS1	NR_040089.1 linkuse as main transcript	n.234-11217C>T	intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ALOX12	ENST00000251535.11 linkuse as main transcript	c.136-69G>A		intron_variant		1	NM_000697.3	ENSP00000251535.6		P18054

Frequencies

GnomAD3 genomes

AF:

0.204

AC:

30966

AN:

152060

Hom.:

3914

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0584

Gnomad AMI

AF:

0.212

Gnomad AMR

AF:

0.159

Gnomad ASJ

AF:

0.267

Gnomad EAS

AF:

0.326

Gnomad SAS

AF:

0.155

Gnomad FIN

AF:

0.266

Gnomad MID

AF:

0.222

Gnomad NFE

AF:

0.282

Gnomad OTH

AF:

0.220

GnomAD4 exome

AF:

0.271

AC:

369898

AN:

1365300

Hom.:

52789

AF XY:

0.268

AC XY:

179123

AN XY:

668940

show subpopulations

Gnomad4 AFR exome

AF:

0.0462

Gnomad4 AMR exome

AF:

0.117

Gnomad4 ASJ exome

AF:

0.273

Gnomad4 EAS exome

AF:

0.298

Gnomad4 SAS exome

AF:

0.152

Gnomad4 FIN exome

AF:

0.256

Gnomad4 NFE exome

AF:

0.292

Gnomad4 OTH exome

AF:

0.263

GnomAD4 genome

AF:

0.203

AC:

30967

AN:

152178

Hom.:

3917

Cov.:

AF XY:

0.202

AC XY:

15032

AN XY:

74398

show subpopulations

Gnomad4 AFR

AF:

0.0583

Gnomad4 AMR

AF:

0.159

Gnomad4 ASJ

AF:

0.267

Gnomad4 EAS

AF:

0.326

Gnomad4 SAS

AF:

0.156

Gnomad4 FIN

AF:

0.266

Gnomad4 NFE

AF:

0.283

Gnomad4 OTH

AF:

0.221

Alfa

AF:

0.264

Hom.:

6762

Bravo

AF:

0.192

Asia WGS

AF:

0.224

AC:

776

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Nov 10, 2018	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

0.67

DANN

Benign

0.75

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.2

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over