Variant 17-6996310-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The NM_000697.3(ALOX12):c.135+58C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.576 in 1,219,326 control chromosomes in the GnomAD database, including 203,251 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.59 ( 26401 hom., cov: 31)

Exomes 𝑓: 0.57 ( 176850 hom. )

Consequence

ALOX12
NM_000697.3 intron

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.302

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 -14 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.78).

BP6

Variant 17-6996310-C-T is Benign according to our data. Variant chr17-6996310-C-T is described in ClinVar as [Benign]. Clinvar id is 1235859.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.648 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	MANE
ALOX12	NM_000697.3 linkuse as main transcript	c.135+58C>T	intron_variant	ENST00000251535.11
ALOX12-AS1	NR_040089.1 linkuse as main transcript	n.234-10770G>A	intron_variant, non_coding_transcript_variant
ALOX12	XM_011523780.3 linkuse as main transcript	c.135+58C>T	intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ALOX12	ENST00000251535.11 linkuse as main transcript	c.135+58C>T		intron_variant		1	NM_000697.3	P1
ALOX12-AS1	ENST00000653385.1 linkuse as main transcript	n.139+15886G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes

AF:

0.590

AC:

89140

AN:

151192

Hom.:

26374

Cov.:

show subpopulations

Gnomad AFR

AF:

0.578

Gnomad AMI

AF:

0.600

Gnomad AMR

AF:

0.659

Gnomad ASJ

AF:

0.541

Gnomad EAS

AF:

0.519

Gnomad SAS

AF:

0.538

Gnomad FIN

AF:

0.657

Gnomad MID

AF:

0.565

Gnomad NFE

AF:

0.582

Gnomad OTH

AF:

0.572

GnomAD4 exome

AF:

0.574

AC:

613569

AN:

1068026

Hom.:

176850

AF XY:

0.575

AC XY:

289932

AN XY:

504666

show subpopulations

Gnomad4 AFR exome

AF:

0.574

Gnomad4 AMR exome

AF:

0.670

Gnomad4 ASJ exome

AF:

0.541

Gnomad4 EAS exome

AF:

0.589

Gnomad4 SAS exome

AF:

0.547

Gnomad4 FIN exome

AF:

0.662

Gnomad4 NFE exome

AF:

0.573

Gnomad4 OTH exome

AF:

0.562

GnomAD4 genome

AF:

0.590

AC:

89213

AN:

151300

Hom.:

26401

Cov.:

AF XY:

0.594

AC XY:

43879

AN XY:

73914

show subpopulations

Gnomad4 AFR

AF:

0.579

Gnomad4 AMR

AF:

0.659

Gnomad4 ASJ

AF:

0.541

Gnomad4 EAS

AF:

0.519

Gnomad4 SAS

AF:

0.538

Gnomad4 FIN

AF:

0.657

Gnomad4 NFE

AF:

0.582

Gnomad4 OTH

AF:

0.572

Alfa

AF:

0.591

Hom.:

3326

Bravo

AF:

0.587

Asia WGS

AF:

0.535

AC:

1862

AN:

3470

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

-0.78

CADD

Benign

8.3

DANN

Benign

0.81

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

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