Variant chr17-7000625-G-A 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.951+146G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.488 in 903,006 control chromosomes in the GnomAD database, including 109,812 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.48 ( 17736 hom., cov: 32)

Exomes 𝑓: 0.49 ( 92076 hom. )

Consequence

ALOX12
NM_000697.3 intron

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.370

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:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.85).

BP6

Variant 17-7000625-G-A is Benign according to our data. Variant chr17-7000625-G-A is described in ClinVar as [Benign]. Clinvar id is 1179701.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.505 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	MANE	Protein	UniProt
ALOX12	NM_000697.3 linkuse as main transcript	c.951+146G>A	intron_variant	ENST00000251535.11	NP_000688.2	P18054
ALOX12	XM_011523780.3 linkuse as main transcript	c.744+146G>A	intron_variant		XP_011522082.2
ALOX12-AS1	NR_040089.1 linkuse as main transcript	n.233+9171C>T	intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ALOX12	ENST00000251535.11 linkuse as main transcript	c.951+146G>A		intron_variant		1	NM_000697.3	ENSP00000251535.6		P18054

Frequencies

GnomAD3 genomes

AF:

0.482

AC:

73087

AN:

151752

Hom.:

17722

Cov.:

show subpopulations

Gnomad AFR

AF:

0.469

Gnomad AMI

AF:

0.467

Gnomad AMR

AF:

0.396

Gnomad ASJ

AF:

0.478

Gnomad EAS

AF:

0.410

Gnomad SAS

AF:

0.497

Gnomad FIN

AF:

0.505

Gnomad MID

AF:

0.522

Gnomad NFE

AF:

0.509

Gnomad OTH

AF:

0.484

GnomAD4 exome

AF:

0.489

AC:

367265

AN:

751136

Hom.:

92076

AF XY:

0.490

AC XY:

186770

AN XY:

381062

show subpopulations

Gnomad4 AFR exome

AF:

0.456

Gnomad4 AMR exome

AF:

0.317

Gnomad4 ASJ exome

AF:

0.479

Gnomad4 EAS exome

AF:

0.460

Gnomad4 SAS exome

AF:

0.505

Gnomad4 FIN exome

AF:

0.519

Gnomad4 NFE exome

AF:

0.496

Gnomad4 OTH exome

AF:

0.479

GnomAD4 genome

AF:

0.482

AC:

73143

AN:

151870

Hom.:

17736

Cov.:

AF XY:

0.480

AC XY:

35637

AN XY:

74178

show subpopulations

Gnomad4 AFR

AF:

0.469

Gnomad4 AMR

AF:

0.395

Gnomad4 ASJ

AF:

0.478

Gnomad4 EAS

AF:

0.411

Gnomad4 SAS

AF:

0.497

Gnomad4 FIN

AF:

0.505

Gnomad4 NFE

AF:

0.509

Gnomad4 OTH

AF:

0.484

Alfa

AF:

0.484

Hom.:

2409

Bravo

AF:

0.466

Asia WGS

AF:

0.442

AC:

1542

AN:

3478

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

-0.85

CADD

Benign

2.2

DANN

Benign

0.57

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