rs312470
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Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_000697.3(ALOX12):c.542+23G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.899 in 1,613,954 control chromosomes in the GnomAD database, including 659,461 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.82 ( 52833 hom., cov: 31)
Exomes 𝑓: 0.91 ( 606628 hom. )
Consequence
ALOX12
NM_000697.3 intron
NM_000697.3 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.0350
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 -14 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.83).
BP6
?
Variant 17-6998860-G-A is Benign according to our data. Variant chr17-6998860-G-A is described in ClinVar as [Benign]. Clinvar id is 1262104.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.928 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ALOX12 | NM_000697.3 | c.542+23G>A | intron_variant | ENST00000251535.11 | |||
ALOX12-AS1 | NR_040089.1 | n.233+10936C>T | intron_variant, non_coding_transcript_variant | ||||
ALOX12 | XM_011523780.3 | c.542+23G>A | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ALOX12 | ENST00000251535.11 | c.542+23G>A | intron_variant | 1 | NM_000697.3 | P1 | |||
ALOX12-AS1 | ENST00000653385.1 | n.139+13336C>T | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes ? AF: 0.824 AC: 125256AN: 152012Hom.: 52812 Cov.: 31
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GnomAD3 exomes AF: 0.847 AC: 212795AN: 251286Hom.: 93297 AF XY: 0.869 AC XY: 118057AN XY: 135826
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GnomAD4 exome AF: 0.907 AC: 1325798AN: 1461824Hom.: 606628 Cov.: 61 AF XY: 0.911 AC XY: 662537AN XY: 727218
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GnomAD4 genome ? AF: 0.824 AC: 125322AN: 152130Hom.: 52833 Cov.: 31 AF XY: 0.821 AC XY: 61030AN XY: 74380
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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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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at