Variant 17-6997125-T-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP6_Very_StrongBA1

The ENST00000251535.11(ALOX12):c.337+98T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.582 in 1,442,712 control chromosomes in the GnomAD database, including 245,361 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.61 ( 28846 hom., cov: 31)

Exomes 𝑓: 0.58 ( 216515 hom. )

Consequence

ALOX12
ENST00000251535.11 intron

Scores

Clinical Significance

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

Conservation

PhyloP100: -0.369

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 -16 ACMG points.

BP6

Variant 17-6997125-T-G is Benign according to our data. Variant chr17-6997125-T-G is described in ClinVar as [Benign]. Clinvar id is 1262015.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.658 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	MANE	Protein	UniProt
ALOX12	NM_000697.3 linkuse as main transcript	c.337+98T>G	intron_variant	ENST00000251535.11	NP_000688.2	P18054
ALOX12	XM_011523780.3 linkuse as main transcript	c.337+98T>G	intron_variant		XP_011522082.2
ALOX12-AS1	NR_040089.1 linkuse as main transcript	n.234-11585A>C	intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ALOX12	ENST00000251535.11 linkuse as main transcript	c.337+98T>G		intron_variant		1	NM_000697.3	ENSP00000251535.6		P18054

Frequencies

GnomAD3 genomes

AF:

0.614

AC:

93218

AN:

151818

Hom.:

28809

Cov.:

show subpopulations

Gnomad AFR

AF:

0.663

Gnomad AMI

AF:

0.600

Gnomad AMR

AF:

0.669

Gnomad ASJ

AF:

0.541

Gnomad EAS

AF:

0.522

Gnomad SAS

AF:

0.538

Gnomad FIN

AF:

0.658

Gnomad MID

AF:

0.563

Gnomad NFE

AF:

0.582

Gnomad OTH

AF:

0.592

GnomAD4 exome

AF:

0.578

AC:

745693

AN:

1290776

Hom.:

216515

Cov.:

AF XY:

0.577

AC XY:

360844

AN XY:

625762

show subpopulations

Gnomad4 AFR exome

AF:

0.663

Gnomad4 AMR exome

AF:

0.682

Gnomad4 ASJ exome

AF:

0.540

Gnomad4 EAS exome

AF:

0.572

Gnomad4 SAS exome

AF:

0.544

Gnomad4 FIN exome

AF:

0.657

Gnomad4 NFE exome

AF:

0.574

Gnomad4 OTH exome

AF:

0.568

GnomAD4 genome

AF:

0.614

AC:

93304

AN:

151936

Hom.:

28846

Cov.:

AF XY:

0.617

AC XY:

45816

AN XY:

74250

show subpopulations

Gnomad4 AFR

AF:

0.664

Gnomad4 AMR

AF:

0.668

Gnomad4 ASJ

AF:

0.541

Gnomad4 EAS

AF:

0.522

Gnomad4 SAS

AF:

0.538

Gnomad4 FIN

AF:

0.658

Gnomad4 NFE

AF:

0.582

Gnomad4 OTH

AF:

0.592

Alfa

AF:

0.581

Hom.:

37369

Bravo

AF:

0.615

Asia WGS

AF:

0.542

AC:

1891

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	clinical testing	GeneDx	Nov 10, 2018	- -
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

-0.81

CADD

Benign

DANN

Benign

0.52

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.33

Details are displayed if max score is > 0.2

DS_DG_spliceai

0.33

Position offset: 0

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