15-90084267-T-C
Variant summary
Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2PM4
The NM_002168.4(IDH2):c.1358A>G(p.Ter453TrpextTer42) variant causes a stop lost change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Synonymous variant affecting the same amino acid position (i.e. *453*) has been classified as Likely benign.
Frequency
Consequence
NM_002168.4 stop_lost
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
IDH2 | NM_002168.4 | c.1358A>G | p.Ter453TrpextTer42 | stop_lost | 11/11 | ENST00000330062.8 | |
IDH2 | NM_001289910.1 | c.1202A>G | p.Ter401TrpextTer42 | stop_lost | 11/11 | ||
IDH2 | NM_001290114.2 | c.968A>G | p.Ter323TrpextTer42 | stop_lost | 9/9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
IDH2 | ENST00000330062.8 | c.1358A>G | p.Ter453TrpextTer42 | stop_lost | 11/11 | 1 | NM_002168.4 | P1 | |
IDH2 | ENST00000540499.2 | c.1202A>G | p.Ter401TrpextTer? | stop_lost | 11/11 | 2 | |||
IDH2 | ENST00000559482.5 | c.938A>G | p.Ter313TrpextTer42 | stop_lost | 8/8 | 5 | |||
IDH2 | ENST00000560061.1 | c.*983A>G | 3_prime_UTR_variant, NMD_transcript_variant | 9/9 | 2 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome Cov.: 30
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
D-2-hydroxyglutaric aciduria 2 Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Nov 13, 2023 | This sequence change disrupts the translational stop signal of the IDH2 mRNA. It is expected to extend the length of the IDH2 protein by 42 additional amino acid residues. This variant is not present in population databases (gnomAD no frequency). This variant has not been reported in the literature in individuals affected with IDH2-related conditions. Experimental studies and prediction algorithms are not available or were not evaluated, and the functional significance of this variant is currently unknown. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
No publications associated with this variant yet.