chr17-6999424-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
NM_000697.3 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -3.21
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]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -15 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.78).
BP6
?
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
?
Synonymous conserved (PhyloP=-3.21 with no splicing effect.
BA1
?
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 |
---|---|---|---|---|---|---|---|
ALOX12 | NM_000697.3 | c.765G>A | p.Ser255= | synonymous_variant | 6/14 | ENST00000251535.11 | |
ALOX12-AS1 | NR_040089.1 | n.233+10372C>T | intron_variant, non_coding_transcript_variant | ||||
ALOX12 | XM_011523780.3 | c.558G>A | p.Ser186= | synonymous_variant | 5/13 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ALOX12 | ENST00000251535.11 | c.765G>A | p.Ser255= | synonymous_variant | 6/14 | 1 | NM_000697.3 | P1 | |
ALOX12-AS1 | ENST00000653385.1 | n.139+12772C>T | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes ? AF: 0.612 AC: 92916AN: 151898Hom.: 28584 Cov.: 32
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GnomAD3 exomes AF: 0.599 AC: 150511AN: 251336Hom.: 45613 AF XY: 0.592 AC XY: 80347AN XY: 135836
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GnomAD4 exome AF: 0.581 AC: 848390AN: 1461074Hom.: 247684 Cov.: 55 AF XY: 0.579 AC XY: 421010AN XY: 726890
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GnomAD4 genome ? AF: 0.612 AC: 92997AN: 152016Hom.: 28616 Cov.: 32 AF XY: 0.615 AC XY: 45699AN XY: 74306
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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
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Name
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at