chr2-208237393-A-ACT
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBA1
The NM_005896.4(IDH1):c.1155-225_1155-224insAG variant causes a intron change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.99 ( 74519 hom., cov: 0)
Consequence
IDH1
NM_005896.4 intron
NM_005896.4 intron
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 0.0220
Genes affected
IDH1 (HGNC:5382): (isocitrate dehydrogenase (NADP(+)) 1) Isocitrate dehydrogenases catalyze the oxidative decarboxylation of isocitrate to 2-oxoglutarate. These enzymes belong to two distinct subclasses, one of which utilizes NAD(+) as the electron acceptor and the other NADP(+). Five isocitrate dehydrogenases have been reported: three NAD(+)-dependent isocitrate dehydrogenases, which localize to the mitochondrial matrix, and two NADP(+)-dependent isocitrate dehydrogenases, one of which is mitochondrial and the other predominantly cytosolic. Each NADP(+)-dependent isozyme is a homodimer. The protein encoded by this gene is the NADP(+)-dependent isocitrate dehydrogenase found in the cytoplasm and peroxisomes. It contains the PTS-1 peroxisomal targeting signal sequence. The presence of this enzyme in peroxisomes suggests roles in the regeneration of NADPH for intraperoxisomal reductions, such as the conversion of 2, 4-dienoyl-CoAs to 3-enoyl-CoAs, as well as in peroxisomal reactions that consume 2-oxoglutarate, namely the alpha-hydroxylation of phytanic acid. The cytoplasmic enzyme serves a significant role in cytoplasmic NADPH production. Alternatively spliced transcript variants encoding the same protein have been found for this gene. [provided by RefSeq, Sep 2013]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -10 ACMG points.
BP6
?
Variant 2-208237393-A-ACT is Benign according to our data. Variant chr2-208237393-A-ACT is described in ClinVar as [Benign]. Clinvar id is 1275091.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.994 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
IDH1 | NM_005896.4 | c.1155-225_1155-224insAG | intron_variant | ENST00000345146.7 | |||
IDH1 | NM_001282386.1 | c.1155-225_1155-224insAG | intron_variant | ||||
IDH1 | NM_001282387.1 | c.1155-225_1155-224insAG | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
IDH1 | ENST00000345146.7 | c.1155-225_1155-224insAG | intron_variant | 1 | NM_005896.4 | P1 | |||
IDH1 | ENST00000415913.5 | c.1155-225_1155-224insAG | intron_variant | 1 | P1 | ||||
IDH1 | ENST00000446179.5 | c.1155-225_1155-224insAG | intron_variant | 1 | P1 | ||||
IDH1 | ENST00000484575.1 | n.617-225_617-224insAG | intron_variant, non_coding_transcript_variant | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.989 AC: 150510AN: 152152Hom.: 74469 Cov.: 0
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GnomAD4 genome ? AF: 0.989 AC: 150619AN: 152270Hom.: 74519 Cov.: 0 AF XY: 0.990 AC XY: 73659AN XY: 74434
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?
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3469
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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 submitter | clinical testing | GeneDx | Jun 19, 2021 | - - |
Computational scores
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Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at