17-8072839-T-TGCGCTGGCGGATGTCGTGTGAGATCTGGTTCAG
Variant summary
Our verdict is Uncertain significance. Variant got 5 ACMG points: 5P and 0B. PM2PM4PP5
The NM_001139.3(ALOX12B):c.2037_2038insCTGAACCAGATCTCACACGACATCCGCCAGCGC(p.Leu669_Arg679dup) variant causes a inframe insertion change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Pathogenic (no stars).
Frequency
Genomes: not found (cov: 32)
Consequence
ALOX12B
NM_001139.3 inframe_insertion
NM_001139.3 inframe_insertion
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 0.131
Genes affected
ALOX12B (HGNC:430): (arachidonate 12-lipoxygenase, 12R type) This gene encodes an enzyme involved in the conversion of arachidonic acid to 12R-hydroxyeicosatetraenoic acid. Mutations in this gene are associated with nonbullous congenital ichthyosiform erythroderma. [provided by RefSeq, Sep 2015]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 5 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
PM4
Nonframeshift variant in NON repetitive region in NM_001139.3.
PP5
Variant 17-8072839-T-TGCGCTGGCGGATGTCGTGTGAGATCTGGTTCAG is Pathogenic according to our data. Variant chr17-8072839-T-TGCGCTGGCGGATGTCGTGTGAGATCTGGTTCAG is described in ClinVar as [Pathogenic]. Clinvar id is 995484.Status of the report is no_assertion_criteria_provided, 0 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ALOX12B | NM_001139.3 | c.2037_2038insCTGAACCAGATCTCACACGACATCCGCCAGCGC | p.Leu669_Arg679dup | inframe_insertion | 15/15 | ENST00000647874.1 | NP_001130.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ALOX12B | ENST00000647874.1 | c.2037_2038insCTGAACCAGATCTCACACGACATCCGCCAGCGC | p.Leu669_Arg679dup | inframe_insertion | 15/15 | NM_001139.3 | ENSP00000497784 | P1 | ||
ALOX12B | ENST00000649809.1 | c.1101_1102insCTGAACCAGATCTCACACGACATCCGCCAGCGC | p.Leu357_Arg367dup | inframe_insertion | 8/8 | ENSP00000496845 | ||||
ALOX12B | ENST00000650441.1 | n.460_461insCTGAACCAGATCTCACACGACATCCGCCAGCGC | non_coding_transcript_exon_variant | 4/4 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 genomes
Cov.:
32
GnomAD4 exome Cov.: 32
GnomAD4 exome
Cov.:
32
GnomAD4 genome Cov.: 32
GnomAD4 genome
Cov.:
32
ClinVar
Significance: Pathogenic
Submissions summary: Pathogenic:1
Revision: no assertion criteria provided
LINK: link
Submissions by phenotype
Autosomal recessive congenital ichthyosis 2 Pathogenic:1
Pathogenic, no assertion criteria provided | clinical testing | Institute for Human Genetics, University Medical Center Freiburg | Jan 07, 2021 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at