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17-7001742-T-G

Variant summary

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

The NM_000697.3(ALOX12):c.1092T>G(p.Thr364=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.578 in 1,613,744 control chromosomes in the GnomAD database, including 271,121 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.59 ( 26225 hom., cov: 31)
Exomes 𝑓: 0.58 ( 244896 hom. )

Consequence

ALOX12
NM_000697.3 synonymous

Scores

2

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -1.75
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=-0.9).
BP6
?
    BP6 - Reputable source recently reports variant as benign, but the evidence is not available to the laboratory to perform an independent evaluation
Variant 17-7001742-T-G is Benign according to our data. Variant chr17-7001742-T-G is described in ClinVar as [Benign]. Clinvar id is 1247877.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=-1.75 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 = 0.644 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
ALOX12NM_000697.3 linkuse as main transcriptc.1092T>G p.Thr364= synonymous_variant 8/14 ENST00000251535.11
ALOX12-AS1NR_040089.1 linkuse as main transcriptn.233+8054A>C intron_variant, non_coding_transcript_variant
ALOX12XM_011523780.3 linkuse as main transcriptc.885T>G p.Thr295= synonymous_variant 7/13

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
ALOX12ENST00000251535.11 linkuse as main transcriptc.1092T>G p.Thr364= synonymous_variant 8/141 NM_000697.3 P1
ALOX12-AS1ENST00000653385.1 linkuse as main transcriptn.139+10454A>C intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.585
AC:
88894
AN:
151862
Hom.:
26193
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.566
Gnomad AMI
AF:
0.600
Gnomad AMR
AF:
0.655
Gnomad ASJ
AF:
0.531
Gnomad EAS
AF:
0.527
Gnomad SAS
AF:
0.540
Gnomad FIN
AF:
0.657
Gnomad MID
AF:
0.554
Gnomad NFE
AF:
0.581
Gnomad OTH
AF:
0.579
GnomAD3 exomes
AF:
0.592
AC:
148784
AN:
251418
Hom.:
44521
AF XY:
0.586
AC XY:
79675
AN XY:
135892
show subpopulations
Gnomad AFR exome
AF:
0.568
Gnomad AMR exome
AF:
0.694
Gnomad ASJ exome
AF:
0.536
Gnomad EAS exome
AF:
0.511
Gnomad SAS exome
AF:
0.546
Gnomad FIN exome
AF:
0.670
Gnomad NFE exome
AF:
0.580
Gnomad OTH exome
AF:
0.581
GnomAD4 exome
AF:
0.578
AC:
844203
AN:
1461764
Hom.:
244896
Cov.:
58
AF XY:
0.576
AC XY:
419157
AN XY:
727194
show subpopulations
Gnomad4 AFR exome
AF:
0.557
Gnomad4 AMR exome
AF:
0.689
Gnomad4 ASJ exome
AF:
0.533
Gnomad4 EAS exome
AF:
0.570
Gnomad4 SAS exome
AF:
0.547
Gnomad4 FIN exome
AF:
0.664
Gnomad4 NFE exome
AF:
0.574
Gnomad4 OTH exome
AF:
0.562
GnomAD4 genome
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.585
AC:
88975
AN:
151980
Hom.:
26225
Cov.:
31
AF XY:
0.590
AC XY:
43798
AN XY:
74290
show subpopulations
Gnomad4 AFR
AF:
0.567
Gnomad4 AMR
AF:
0.655
Gnomad4 ASJ
AF:
0.531
Gnomad4 EAS
AF:
0.527
Gnomad4 SAS
AF:
0.540
Gnomad4 FIN
AF:
0.657
Gnomad4 NFE
AF:
0.581
Gnomad4 OTH
AF:
0.579
Alfa
AF:
0.576
Hom.:
30968
Bravo
AF:
0.583
Asia WGS
AF:
0.533
AC:
1857
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
-0.90
Cadd
Benign
0.52
Dann
Benign
0.30

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: rs1042357; hg19: chr17-6905061; COSMIC: COSV52349144; COSMIC: COSV52349144; API