Variant chr17-6998860-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 ENST00000251535.11(ALOX12):c.542+23G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.899 in 1,613,954 control chromosomes in the GnomAD database, including 659,461 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.82 ( 52833 hom., cov: 31)

Exomes 𝑓: 0.91 ( 606628 hom. )

Consequence

ALOX12
ENST00000251535.11 intron

Scores

Clinical Significance

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

Conservation

PhyloP100: 0.0350

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:

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=-0.83).

BP6

Variant 17-6998860-G-A is Benign according to our data. Variant chr17-6998860-G-A is described in ClinVar as [Benign]. Clinvar id is 1262104.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.928 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	MANE	Protein	UniProt
ALOX12	NM_000697.3 linkuse as main transcript	c.542+23G>A	intron_variant	ENST00000251535.11	NP_000688.2	P18054
ALOX12	XM_011523780.3 linkuse as main transcript	c.542+23G>A	intron_variant		XP_011522082.2
ALOX12-AS1	NR_040089.1 linkuse as main transcript	n.233+10936C>T	intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ALOX12	ENST00000251535.11 linkuse as main transcript	c.542+23G>A		intron_variant		1	NM_000697.3	ENSP00000251535.6		P18054

Frequencies

GnomAD3 genomes

AF:

0.824

AC:

125256

AN:

152012

Hom.:

52812

Cov.:

show subpopulations

Gnomad AFR

AF:

0.670

Gnomad AMI

AF:

0.867

Gnomad AMR

AF:

0.670

Gnomad ASJ

AF:

0.934

Gnomad EAS

AF:

0.879

Gnomad SAS

AF:

0.950

Gnomad FIN

AF:

0.848

Gnomad MID

AF:

0.959

Gnomad NFE

AF:

0.927

Gnomad OTH

AF:

0.852

GnomAD3 exomes

AF:

0.847

AC:

212795

AN:

251286

Hom.:

93297

AF XY:

0.869

AC XY:

118057

AN XY:

135826

show subpopulations

Gnomad AFR exome

AF:

0.658

Gnomad AMR exome

AF:

0.512

Gnomad ASJ exome

AF:

0.941

Gnomad EAS exome

AF:

0.878

Gnomad SAS exome

AF:

0.958

Gnomad FIN exome

AF:

0.856

Gnomad NFE exome

AF:

0.929

Gnomad OTH exome

AF:

0.875

GnomAD4 exome

AF:

0.907

AC:

1325798

AN:

1461824

Hom.:

606628

Cov.:

AF XY:

0.911

AC XY:

662537

AN XY:

727218

show subpopulations

Gnomad4 AFR exome

AF:

0.653

Gnomad4 AMR exome

AF:

0.530

Gnomad4 ASJ exome

AF:

0.939

Gnomad4 EAS exome

AF:

0.881

Gnomad4 SAS exome

AF:

0.957

Gnomad4 FIN exome

AF:

0.861

Gnomad4 NFE exome

AF:

0.928

Gnomad4 OTH exome

AF:

0.900

GnomAD4 genome

AF:

0.824

AC:

125322

AN:

152130

Hom.:

52833

Cov.:

AF XY:

0.821

AC XY:

61030

AN XY:

74380

show subpopulations

Gnomad4 AFR

AF:

0.670

Gnomad4 AMR

AF:

0.669

Gnomad4 ASJ

AF:

0.934

Gnomad4 EAS

AF:

0.879

Gnomad4 SAS

AF:

0.951

Gnomad4 FIN

AF:

0.848

Gnomad4 NFE

AF:

0.927

Gnomad4 OTH

AF:

0.853

Alfa

AF:

0.858

Hom.:

12075

Bravo

AF:

0.796

Asia WGS

AF:

0.873

AC:

3037

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

-0.83

CADD

Benign

6.3

DANN

Benign

0.69

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