Variant rs312462 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.1902G>A(p.Leu634=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.103 in 1,614,104 control chromosomes in the GnomAD database, including 9,673 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.091 ( 743 hom., cov: 32)

Exomes 𝑓: 0.10 ( 8930 hom. )

Consequence

ALOX12
NM_000697.3 synonymous

Scores

Clinical Significance

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

Conservation

PhyloP100: -0.258

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=-0.8).

BP6

Variant 17-7010333-G-A is Benign according to our data. Variant chr17-7010333-G-A is described in ClinVar as [Benign]. Clinvar id is 1276383.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=-0.258 with no splicing effect.

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.211 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein
ALOX12	NM_000697.3 linkuse as main transcript	c.1902G>A	p.Leu634=	synonymous_variant	14/14	ENST00000251535.11	NP_000688.2
ALOX12-AS1	NR_040089.1 linkuse as main transcript	n.140-444C>T		intron_variant, non_coding_transcript_variant
ALOX12	XM_011523780.3 linkuse as main transcript	c.1695G>A	p.Leu565=	synonymous_variant	13/13		XP_011522082.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ALOX12	ENST00000251535.11 linkuse as main transcript	c.1902G>A	p.Leu634=	synonymous_variant	14/14	1	NM_000697.3	ENSP00000251535	P1
ALOX12-AS1	ENST00000653385.1 linkuse as main transcript	n.139+1863C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes

AF:

0.0910

AC:

13847

AN:

152122

Hom.:

745

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0654

Gnomad AMI

AF:

0.157

Gnomad AMR

AF:

0.0806

Gnomad ASJ

AF:

0.151

Gnomad EAS

AF:

0.145

Gnomad SAS

AF:

0.223

Gnomad FIN

AF:

0.0542

Gnomad MID

AF:

0.130

Gnomad NFE

AF:

0.0969

Gnomad OTH

AF:

0.0969

GnomAD3 exomes

AF:

0.113

AC:

28395

AN:

251392

Hom.:

1951

AF XY:

0.119

AC XY:

16141

AN XY:

135892

show subpopulations

Gnomad AFR exome

AF:

0.0656

Gnomad AMR exome

AF:

0.102

Gnomad ASJ exome

AF:

0.145

Gnomad EAS exome

AF:

0.149

Gnomad SAS exome

AF:

0.216

Gnomad FIN exome

AF:

0.0571

Gnomad NFE exome

AF:

0.0970

Gnomad OTH exome

AF:

0.116

GnomAD4 exome

AF:

0.104

AC:

152322

AN:

1461864

Hom.:

8930

Cov.:

AF XY:

0.108

AC XY:

78580

AN XY:

727232

show subpopulations

Gnomad4 AFR exome

AF:

0.0671

Gnomad4 AMR exome

AF:

0.0991

Gnomad4 ASJ exome

AF:

0.144

Gnomad4 EAS exome

AF:

0.133

Gnomad4 SAS exome

AF:

0.214

Gnomad4 FIN exome

AF:

0.0592

Gnomad4 NFE exome

AF:

0.0966

Gnomad4 OTH exome

AF:

0.110

GnomAD4 genome

AF:

0.0910

AC:

13849

AN:

152240

Hom.:

743

Cov.:

AF XY:

0.0919

AC XY:

6841

AN XY:

74442

show subpopulations

Gnomad4 AFR

AF:

0.0655

Gnomad4 AMR

AF:

0.0805

Gnomad4 ASJ

AF:

0.151

Gnomad4 EAS

AF:

0.145

Gnomad4 SAS

AF:

0.222

Gnomad4 FIN

AF:

0.0542

Gnomad4 NFE

AF:

0.0969

Gnomad4 OTH

AF:

0.0964

Alfa

AF:

0.101

Hom.:

876

Bravo

AF:

0.0905

Asia WGS

AF:

0.166

AC:

578

AN:

3478

EpiCase

AF:

0.103

EpiControl

AF:

0.103

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	clinical testing	GeneDx	Jun 09, 2021	- -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.80

CADD

Benign

5.9

DANN

Benign

0.79

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