Variant 17-6997043-C-T 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.337+16C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.583 in 1,522,744 control chromosomes in the GnomAD database, including 260,078 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.61 ( 28859 hom., cov: 33)

Exomes 𝑓: 0.58 ( 231219 hom. )

Consequence

ALOX12
NM_000697.3 intron

Scores

Clinical Significance

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

Conservation

PhyloP100: -1.35

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:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.79).

BP6

Variant 17-6997043-C-T is Benign according to our data. Variant chr17-6997043-C-T is described in ClinVar as [Benign]. Clinvar id is 1289083.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.657 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	MANE	Protein
ALOX12	NM_000697.3 linkuse as main transcript	c.337+16C>T	intron_variant	ENST00000251535.11	NP_000688.2
ALOX12-AS1	NR_040089.1 linkuse as main transcript	n.234-11503G>A	intron_variant, non_coding_transcript_variant
ALOX12	XM_011523780.3 linkuse as main transcript	c.337+16C>T	intron_variant		XP_011522082.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ALOX12	ENST00000251535.11 linkuse as main transcript	c.337+16C>T		intron_variant		1	NM_000697.3	ENSP00000251535	P1
ALOX12-AS1	ENST00000653385.1 linkuse as main transcript	n.139+15153G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes

AF:

0.614

AC:

93277

AN:

151994

Hom.:

28822

Cov.:

show subpopulations

Gnomad AFR

AF:

0.663

Gnomad AMI

AF:

0.600

Gnomad AMR

AF:

0.668

Gnomad ASJ

AF:

0.542

Gnomad EAS

AF:

0.522

Gnomad SAS

AF:

0.537

Gnomad FIN

AF:

0.658

Gnomad MID

AF:

0.563

Gnomad NFE

AF:

0.582

Gnomad OTH

AF:

0.594

GnomAD3 exomes

AF:

0.600

AC:

84535

AN:

140788

Hom.:

25719

AF XY:

0.590

AC XY:

44278

AN XY:

74990

show subpopulations

Gnomad AFR exome

AF:

0.678

Gnomad AMR exome

AF:

0.694

Gnomad ASJ exome

AF:

0.549

Gnomad EAS exome

AF:

0.511

Gnomad SAS exome

AF:

0.547

Gnomad FIN exome

AF:

0.675

Gnomad NFE exome

AF:

0.583

Gnomad OTH exome

AF:

0.586

GnomAD4 exome

AF:

0.579

AC:

794111

AN:

1370632

Hom.:

231219

Cov.:

AF XY:

0.578

AC XY:

388632

AN XY:

672192

show subpopulations

Gnomad4 AFR exome

AF:

0.665

Gnomad4 AMR exome

AF:

0.690

Gnomad4 ASJ exome

AF:

0.542

Gnomad4 EAS exome

AF:

0.572

Gnomad4 SAS exome

AF:

0.546

Gnomad4 FIN exome

AF:

0.661

Gnomad4 NFE exome

AF:

0.574

Gnomad4 OTH exome

AF:

0.569

GnomAD4 genome

AF:

0.614

AC:

93363

AN:

152112

Hom.:

28859

Cov.:

AF XY:

0.617

AC XY:

45881

AN XY:

74366

show subpopulations

Gnomad4 AFR

AF:

0.663

Gnomad4 AMR

AF:

0.668

Gnomad4 ASJ

AF:

0.542

Gnomad4 EAS

AF:

0.521

Gnomad4 SAS

AF:

0.538

Gnomad4 FIN

AF:

0.658

Gnomad4 NFE

AF:

0.582

Gnomad4 OTH

AF:

0.594

Alfa

AF:

0.590

Hom.:

5007

Bravo

AF:

0.615

Asia WGS

AF:

0.541

AC:

1885

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

-0.79

CADD

Benign

0.58

DANN

Benign

0.86

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