rs1227626398
Variant summary
Our verdict is Uncertain significance. Variant got 5 ACMG points: 6P and 1B. PM2PP3_StrongBP6
The NM_002168.4(IDH2):c.695C>T(p.Ala232Val) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000137 in 1,461,278 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_002168.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
IDH2 | NM_002168.4 | c.695C>T | p.Ala232Val | missense_variant | 6/11 | ENST00000330062.8 | |
IDH2 | NM_001289910.1 | c.539C>T | p.Ala180Val | missense_variant | 6/11 | ||
IDH2 | NM_001290114.2 | c.305C>T | p.Ala102Val | missense_variant | 4/9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
IDH2 | ENST00000330062.8 | c.695C>T | p.Ala232Val | missense_variant | 6/11 | 1 | NM_002168.4 | P1 | |
IDH2 | ENST00000540499.2 | c.539C>T | p.Ala180Val | missense_variant | 6/11 | 2 | |||
IDH2 | ENST00000559482.5 | c.368C>T | p.Ala123Val | missense_variant | 4/8 | 5 | |||
IDH2 | ENST00000560061.1 | c.*320C>T | 3_prime_UTR_variant, NMD_transcript_variant | 4/9 | 2 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD3 exomes AF: 0.00000398 AC: 1AN: 251470Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135910
GnomAD4 exome AF: 0.00000137 AC: 2AN: 1461278Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 726944
GnomAD4 genome ? Cov.: 32
ClinVar
Submissions by phenotype
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | GeneDx | Jan 12, 2021 | In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; Has not been previously published as pathogenic or benign to our knowledge - |
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Nov 16, 2016 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at