NM_002168.4:c.327G>A
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_ModerateBP6BP7BS1BS2
The NM_002168.4(IDH2):c.327G>A(p.Val109Val) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00375 in 1,614,162 control chromosomes in the GnomAD database, including 13 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_002168.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -12 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
IDH2 | NM_002168.4 | c.327G>A | p.Val109Val | synonymous_variant | Exon 3 of 11 | ENST00000330062.8 | NP_002159.2 | |
IDH2 | NM_001289910.1 | c.171G>A | p.Val57Val | synonymous_variant | Exon 3 of 11 | NP_001276839.1 | ||
IDH2 | NM_001290114.2 | c.-17-1778G>A | intron_variant | Intron 1 of 8 | NP_001277043.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
IDH2 | ENST00000330062.8 | c.327G>A | p.Val109Val | synonymous_variant | Exon 3 of 11 | 1 | NM_002168.4 | ENSP00000331897.4 | ||
IDH2 | ENST00000540499.2 | c.171G>A | p.Val57Val | synonymous_variant | Exon 3 of 11 | 2 | ENSP00000446147.2 | |||
IDH2 | ENST00000559482.5 | c.207+1028G>A | intron_variant | Intron 2 of 7 | 5 | ENSP00000453016.1 | ||||
IDH2 | ENST00000560061.1 | n.116-1778G>A | intron_variant | Intron 1 of 8 | 2 | ENSP00000453254.1 |
Frequencies
GnomAD3 genomes AF: 0.00244 AC: 371AN: 152222Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.00247 AC: 621AN: 251372Hom.: 0 AF XY: 0.00243 AC XY: 330AN XY: 135884
GnomAD4 exome AF: 0.00388 AC: 5679AN: 1461822Hom.: 13 Cov.: 32 AF XY: 0.00362 AC XY: 2633AN XY: 727202
GnomAD4 genome AF: 0.00243 AC: 370AN: 152340Hom.: 0 Cov.: 33 AF XY: 0.00228 AC XY: 170AN XY: 74498
ClinVar
Submissions by phenotype
not specified Uncertain:1
- -
not provided Benign:1
IDH2: BP4, BP7, BS2 -
D-2-hydroxyglutaric aciduria 2 Benign:1
- -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at