2-208248389-G-T
Variant summary
Our verdict is Likely pathogenic. Variant got 8 ACMG points: 8P and 0B. PM2PM5PP3_ModeratePP5_Moderate
The NM_005896.4(IDH1):c.394C>A(p.Arg132Ser) variant causes a missense change. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Pathogenic (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R132C) has been classified as Pathogenic.
Frequency
Consequence
NM_005896.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
IDH1 | NM_005896.4 | c.394C>A | p.Arg132Ser | missense_variant | Exon 4 of 10 | ENST00000345146.7 | NP_005887.2 | |
IDH1 | NM_001282386.1 | c.394C>A | p.Arg132Ser | missense_variant | Exon 4 of 10 | NP_001269315.1 | ||
IDH1 | NM_001282387.1 | c.394C>A | p.Arg132Ser | missense_variant | Exon 4 of 10 | NP_001269316.1 |
Ensembl
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 1461688Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 727166
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not provided Pathogenic:1
IDH1: PM1, PM2, PM5, PS4:Moderate, PP3, PS3:Supporting -
Neoplasm Other:1
- -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at