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17-6999424-G-A

Variant summary

Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BA1

The NM_000697.3(ALOX12):c.765G>A(p.Ser255=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.584 in 1,613,090 control chromosomes in the GnomAD database, including 276,300 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.61 ( 28616 hom., cov: 32)
Exomes 𝑓: 0.58 ( 247684 hom. )

Consequence

ALOX12
NM_000697.3 synonymous

Scores

2

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -3.21
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-AS1 (HGNC:51342): (ALOX12 antisense RNA 1)

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -15 ACMG points.

BP4
?
    BP4 - Multiple lines of computational evidence suggest no impact on gene or gene product (conservation, evolutionary, splicing impact, etc.)
Computational evidence support a benign effect (BayesDel_noAF=-0.78).
BP6
?
    BP6 - Reputable source recently reports variant as benign, but the evidence is not available to the laboratory to perform an independent evaluation
Variant 17-6999424-G-A is Benign according to our data. Variant chr17-6999424-G-A is described in ClinVar as [Benign]. Clinvar id is 1259628.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
    BP7 - A synonymous (silent) variant for which splicing prediction algorithms predict no impact to the splice consensus sequence nor the creation of a new splice site AND the nucleotide is not highly conserved
Synonymous conserved (PhyloP=-3.21 with no splicing effect.
BA1
?
    BA1 - Allele frequency is >5% in Exome Sequencing Project, 1000 Genomes Project, or Exome Aggregation Consortium
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.657 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
ALOX12NM_000697.3 linkuse as main transcriptc.765G>A p.Ser255= synonymous_variant 6/14 ENST00000251535.11
ALOX12-AS1NR_040089.1 linkuse as main transcriptn.233+10372C>T intron_variant, non_coding_transcript_variant
ALOX12XM_011523780.3 linkuse as main transcriptc.558G>A p.Ser186= synonymous_variant 5/13

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
ALOX12ENST00000251535.11 linkuse as main transcriptc.765G>A p.Ser255= synonymous_variant 6/141 NM_000697.3 P1
ALOX12-AS1ENST00000653385.1 linkuse as main transcriptn.139+12772C>T intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.612
AC:
92916
AN:
151898
Hom.:
28584
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.656
Gnomad AMI
AF:
0.599
Gnomad AMR
AF:
0.668
Gnomad ASJ
AF:
0.544
Gnomad EAS
AF:
0.524
Gnomad SAS
AF:
0.538
Gnomad FIN
AF:
0.657
Gnomad MID
AF:
0.566
Gnomad NFE
AF:
0.581
Gnomad OTH
AF:
0.594
GnomAD3 exomes
AF:
0.599
AC:
150511
AN:
251336
Hom.:
45613
AF XY:
0.592
AC XY:
80347
AN XY:
135836
show subpopulations
Gnomad AFR exome
AF:
0.659
Gnomad AMR exome
AF:
0.698
Gnomad ASJ exome
AF:
0.548
Gnomad EAS exome
AF:
0.509
Gnomad SAS exome
AF:
0.546
Gnomad FIN exome
AF:
0.670
Gnomad NFE exome
AF:
0.580
Gnomad OTH exome
AF:
0.586
GnomAD4 exome
AF:
0.581
AC:
848390
AN:
1461074
Hom.:
247684
Cov.:
55
AF XY:
0.579
AC XY:
421010
AN XY:
726890
show subpopulations
Gnomad4 AFR exome
AF:
0.655
Gnomad4 AMR exome
AF:
0.694
Gnomad4 ASJ exome
AF:
0.545
Gnomad4 EAS exome
AF:
0.568
Gnomad4 SAS exome
AF:
0.546
Gnomad4 FIN exome
AF:
0.664
Gnomad4 NFE exome
AF:
0.574
Gnomad4 OTH exome
AF:
0.570
GnomAD4 genome
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.612
AC:
92997
AN:
152016
Hom.:
28616
Cov.:
32
AF XY:
0.615
AC XY:
45699
AN XY:
74306
show subpopulations
Gnomad4 AFR
AF:
0.656
Gnomad4 AMR
AF:
0.668
Gnomad4 ASJ
AF:
0.544
Gnomad4 EAS
AF:
0.523
Gnomad4 SAS
AF:
0.538
Gnomad4 FIN
AF:
0.657
Gnomad4 NFE
AF:
0.581
Gnomad4 OTH
AF:
0.594
Alfa
AF:
0.592
Hom.:
19457
Bravo
AF:
0.613
Asia WGS
AF:
0.541
AC:
1885
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 submitterclinical testingGeneDxNov 10, 2018- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.78
Cadd
Benign
0.10
Dann
Benign
0.82

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.010
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.

Other links and lift over

dbSNP: rs1042356; hg19: chr17-6902743; COSMIC: COSV52350197; COSMIC: COSV52350197; API