Variant 17-6996240-C-G 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.123C>G(p.Pro41=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.991 in 1,245,516 control chromosomes in the GnomAD database, including 611,800 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.96 ( 69848 hom., cov: 33)

Exomes 𝑓: 1.0 ( 541952 hom. )

Consequence

ALOX12
NM_000697.3 synonymous

Scores

Clinical Significance

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

Conservation

PhyloP100: -2.10

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 -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.73).

BP6

Variant 17-6996240-C-G is Benign according to our data. Variant chr17-6996240-C-G is described in ClinVar as [Benign]. Clinvar id is 1269497.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=-2.1 with no splicing effect.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.993 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.123C>G	p.Pro41=	synonymous_variant	1/14	ENST00000251535.11	NP_000688.2
ALOX12-AS1	NR_040089.1 linkuse as main transcript	n.234-10700G>C		intron_variant, non_coding_transcript_variant
ALOX12	XM_011523780.3 linkuse as main transcript	c.123C>G	p.Pro41=	synonymous_variant	1/13		XP_011522082.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ALOX12	ENST00000251535.11 linkuse as main transcript	c.123C>G	p.Pro41=	synonymous_variant	1/14	1	NM_000697.3	ENSP00000251535	P1
ALOX12-AS1	ENST00000653385.1 linkuse as main transcript	n.139+15956G>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes

AF:

0.957

AC:

145456

AN:

152058

Hom.:

69812

Cov.:

show subpopulations

Gnomad AFR

AF:

0.866

Gnomad AMI

AF:

1.00

Gnomad AMR

AF:

0.942

Gnomad ASJ

AF:

1.00

Gnomad EAS

AF:

0.994

Gnomad SAS

AF:

0.996

Gnomad FIN

AF:

1.00

Gnomad MID

AF:

1.00

Gnomad NFE

AF:

0.999

Gnomad OTH

AF:

0.960

GnomAD3 exomes

AF:

0.997

AC:

8851

AN:

8874

Hom.:

4416

AF XY:

0.998

AC XY:

4412

AN XY:

4422

show subpopulations

Gnomad AFR exome

AF:

0.804

Gnomad AMR exome

AF:

1.00

Gnomad ASJ exome

AF:

1.00

Gnomad EAS exome

AF:

0.980

Gnomad SAS exome

AF:

1.00

Gnomad FIN exome

AF:

1.00

Gnomad NFE exome

AF:

0.999

Gnomad OTH exome

AF:

1.00

GnomAD4 exome

AF:

0.995

AC:

1088361

AN:

1093350

Hom.:

541952

Cov.:

AF XY:

0.996

AC XY:

515261

AN XY:

517398

show subpopulations

Gnomad4 AFR exome

AF:

0.858

Gnomad4 AMR exome

AF:

0.927

Gnomad4 ASJ exome

AF:

1.00

Gnomad4 EAS exome

AF:

0.995

Gnomad4 SAS exome

AF:

0.996

Gnomad4 FIN exome

AF:

1.00

Gnomad4 NFE exome

AF:

1.00

Gnomad4 OTH exome

AF:

0.987

GnomAD4 genome

AF:

0.956

AC:

145546

AN:

152166

Hom.:

69848

Cov.:

AF XY:

0.957

AC XY:

71209

AN XY:

74384

show subpopulations

Gnomad4 AFR

AF:

0.866

Gnomad4 AMR

AF:

0.941

Gnomad4 ASJ

AF:

1.00

Gnomad4 EAS

AF:

0.994

Gnomad4 SAS

AF:

0.996

Gnomad4 FIN

AF:

1.00

Gnomad4 NFE

AF:

0.999

Gnomad4 OTH

AF:

0.961

Alfa

AF:

0.989

Hom.:

3490

Bravo

AF:

0.948

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

-0.73

CADD

Benign

0.19

DANN

Benign

0.83

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