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GeneBe

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

Scores

Not classified

Clinical Significance

Pathogenic no assertion criteria provided P:1

Conservation

PhyloP100: 0.131
Variant links:
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
?
    PM2 - Absent from controls (or at extremely low frequency if recessive) in Exome Sequencing Project, 1000 Genomes Project, or Exome Aggregation Consortium
Very rare variant in population databases, with high coverage;
PM4
?
    PM4 - Protein length changes as a result of in-frame deletions/insertions in a nonrepeat region or stop-loss variants
Nonframeshift variant in NON repetitive region in NM_001139.3.
PP5
?
    PP5 - Reputable source recently reports variant as pathogenic, but the evidence is not available to the laboratory to perform an independent evaluation
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 UniProt
ALOX12BNM_001139.3 linkuse as main transcriptc.2037_2038insCTGAACCAGATCTCACACGACATCCGCCAGCGC p.Leu669_Arg679dup inframe_insertion 15/15 ENST00000647874.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
ALOX12BENST00000647874.1 linkuse as main transcriptc.2037_2038insCTGAACCAGATCTCACACGACATCCGCCAGCGC p.Leu669_Arg679dup inframe_insertion 15/15 NM_001139.3 P1
ALOX12BENST00000649809.1 linkuse as main transcriptc.1101_1102insCTGAACCAGATCTCACACGACATCCGCCAGCGC p.Leu357_Arg367dup inframe_insertion 8/8
ALOX12BENST00000650441.1 linkuse as main transcriptn.460_461insCTGAACCAGATCTCACACGACATCCGCCAGCGC non_coding_transcript_exon_variant 4/4

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
Cov.:
32
GnomAD4 exome
Cov.:
32
GnomAD4 genome
?
    Genome Aggregation Database, over 76,156 genomes
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 providedclinical testingInstitute for Human Genetics, University Medical Center FreiburgJan 07, 2021- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction

Splicing

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: rs1977008747; hg19: chr17-7976157; API