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rs2307214

Positions:

Variant summary

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

The NM_000697.3(ALOX12):ā€‹c.1452A>Gā€‹(p.Gln484=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0796 in 1,613,512 control chromosomes in the GnomAD database, including 8,544 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā˜…).

Frequency

Genomes: š‘“ 0.079 ( 866 hom., cov: 31)
Exomes š‘“: 0.080 ( 7678 hom. )

Consequence

ALOX12
NM_000697.3 synonymous

Scores

2

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.756
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=-0.89).
BP6
?
    BP6 - Reputable source recently reports variant as benign, but the evidence is not available to the laboratory to perform an independent evaluation
Variant 17-7006519-A-G is Benign according to our data. Variant chr17-7006519-A-G is described in ClinVar as [Benign]. Clinvar id is 1234828.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=-0.756 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 = 0.239 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
ALOX12NM_000697.3 linkuse as main transcriptc.1452A>G p.Gln484= synonymous_variant 11/14 ENST00000251535.11
ALOX12-AS1NR_040089.1 linkuse as main transcriptn.233+3277T>C intron_variant, non_coding_transcript_variant
ALOX12XM_011523780.3 linkuse as main transcriptc.1245A>G p.Gln415= synonymous_variant 10/13

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
ALOX12ENST00000251535.11 linkuse as main transcriptc.1452A>G p.Gln484= synonymous_variant 11/141 NM_000697.3 P1
ALOX12-AS1ENST00000653385.1 linkuse as main transcriptn.139+5677T>C intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.0793
AC:
12054
AN:
151982
Hom.:
863
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.0170
Gnomad AMI
AF:
0.133
Gnomad AMR
AF:
0.245
Gnomad ASJ
AF:
0.0493
Gnomad EAS
AF:
0.114
Gnomad SAS
AF:
0.0405
Gnomad FIN
AF:
0.151
Gnomad MID
AF:
0.0127
Gnomad NFE
AF:
0.0705
Gnomad OTH
AF:
0.0718
GnomAD3 exomes
AF:
0.117
AC:
29443
AN:
250980
Hom.:
3876
AF XY:
0.104
AC XY:
14077
AN XY:
135642
show subpopulations
Gnomad AFR exome
AF:
0.0158
Gnomad AMR exome
AF:
0.408
Gnomad ASJ exome
AF:
0.0430
Gnomad EAS exome
AF:
0.114
Gnomad SAS exome
AF:
0.0345
Gnomad FIN exome
AF:
0.142
Gnomad NFE exome
AF:
0.0692
Gnomad OTH exome
AF:
0.0991
GnomAD4 exome
AF:
0.0797
AC:
116421
AN:
1461412
Hom.:
7678
Cov.:
32
AF XY:
0.0771
AC XY:
56041
AN XY:
727002
show subpopulations
Gnomad4 AFR exome
AF:
0.0119
Gnomad4 AMR exome
AF:
0.390
Gnomad4 ASJ exome
AF:
0.0449
Gnomad4 EAS exome
AF:
0.114
Gnomad4 SAS exome
AF:
0.0357
Gnomad4 FIN exome
AF:
0.137
Gnomad4 NFE exome
AF:
0.0703
Gnomad4 OTH exome
AF:
0.0715
GnomAD4 genome
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.0793
AC:
12061
AN:
152100
Hom.:
866
Cov.:
31
AF XY:
0.0858
AC XY:
6374
AN XY:
74332
show subpopulations
Gnomad4 AFR
AF:
0.0170
Gnomad4 AMR
AF:
0.246
Gnomad4 ASJ
AF:
0.0493
Gnomad4 EAS
AF:
0.113
Gnomad4 SAS
AF:
0.0399
Gnomad4 FIN
AF:
0.151
Gnomad4 NFE
AF:
0.0704
Gnomad4 OTH
AF:
0.0706
Alfa
AF:
0.0643
Hom.:
507
Bravo
AF:
0.0888
Asia WGS
AF:
0.0690
AC:
238
AN:
3478
EpiCase
AF:
0.0642
EpiControl
AF:
0.0604

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
-0.89
CADD
Benign
2.8
DANN
Benign
0.74

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.

Other links and lift over

dbSNP: rs2307214; hg19: chr17-6909838; COSMIC: COSV52349664; COSMIC: COSV52349664; API