Variant chr17-7006519-A-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1

The NM_000697.3(ALOX12):c.1452A>G(p.Gln484=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0796 in 1,613,512 control chromosomes in the GnomAD database, including 8,544 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.079 ( 866 hom., cov: 31)

Exomes 𝑓: 0.080 ( 7678 hom. )

Consequence

ALOX12
NM_000697.3 synonymous

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.756

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: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 -21 ACMG points.

BP4

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

BP6

Variant 17-7006519-A-G is Benign according to our data. Variant chr17-7006519-A-G is described in ClinVar as [Benign]. Clinvar id is 1234828.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=-0.756 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.239 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE
ALOX12	NM_000697.3 linkuse as main transcript	c.1452A>G	p.Gln484=	synonymous_variant	11/14	ENST00000251535.11
ALOX12-AS1	NR_040089.1 linkuse as main transcript	n.233+3277T>C		intron_variant, non_coding_transcript_variant
ALOX12	XM_011523780.3 linkuse as main transcript	c.1245A>G	p.Gln415=	synonymous_variant	10/13

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ALOX12	ENST00000251535.11 linkuse as main transcript	c.1452A>G	p.Gln484=	synonymous_variant	11/14	1	NM_000697.3	P1
ALOX12-AS1	ENST00000653385.1 linkuse as main transcript	n.139+5677T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes

AF:

0.0793

AC:

12054

AN:

151982

Hom.:

863

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0170

Gnomad AMI

AF:

0.133

Gnomad AMR

AF:

0.245

Gnomad ASJ

AF:

0.0493

Gnomad EAS

AF:

0.114

Gnomad SAS

AF:

0.0405

Gnomad FIN

AF:

0.151

Gnomad MID

AF:

0.0127

Gnomad NFE

AF:

0.0705

Gnomad OTH

AF:

0.0718

GnomAD3 exomes

AF:

0.117

AC:

29443

AN:

250980

Hom.:

3876

AF XY:

0.104

AC XY:

14077

AN XY:

135642

show subpopulations

Gnomad AFR exome

AF:

0.0158

Gnomad AMR exome

AF:

0.408

Gnomad ASJ exome

AF:

0.0430

Gnomad EAS exome

AF:

0.114

Gnomad SAS exome

AF:

0.0345

Gnomad FIN exome

AF:

0.142

Gnomad NFE exome

AF:

0.0692

Gnomad OTH exome

AF:

0.0991

GnomAD4 exome

AF:

0.0797

AC:

116421

AN:

1461412

Hom.:

7678

Cov.:

AF XY:

0.0771

AC XY:

56041

AN XY:

727002

show subpopulations

Gnomad4 AFR exome

AF:

0.0119

Gnomad4 AMR exome

AF:

0.390

Gnomad4 ASJ exome

AF:

0.0449

Gnomad4 EAS exome

AF:

0.114

Gnomad4 SAS exome

AF:

0.0357

Gnomad4 FIN exome

AF:

0.137

Gnomad4 NFE exome

AF:

0.0703

Gnomad4 OTH exome

AF:

0.0715

GnomAD4 genome

AF:

0.0793

AC:

12061

AN:

152100

Hom.:

866

Cov.:

AF XY:

0.0858

AC XY:

6374

AN XY:

74332

show subpopulations

Gnomad4 AFR

AF:

0.0170

Gnomad4 AMR

AF:

0.246

Gnomad4 ASJ

AF:

0.0493

Gnomad4 EAS

AF:

0.113

Gnomad4 SAS

AF:

0.0399

Gnomad4 FIN

AF:

0.151

Gnomad4 NFE

AF:

0.0704

Gnomad4 OTH

AF:

0.0706

Alfa

AF:

0.0643

Hom.:

507

Bravo

AF:

0.0888

Asia WGS

AF:

0.0690

AC:

238

AN:

3478

EpiCase

AF:

0.0642

EpiControl

AF:

0.0604

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

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

2.8

DANN

Benign

0.74

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