15-90088692-C-T
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_StrongBP7BS2_Supporting
The NM_002168.4(IDH2):c.429G>A(p.Leu143=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000041 in 1,461,884 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Synonymous variant affecting the same amino acid position (i.e. L143L) has been classified as Likely benign.
Frequency
Consequence
NM_002168.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
IDH2 | NM_002168.4 | c.429G>A | p.Leu143= | synonymous_variant | 4/11 | ENST00000330062.8 | |
IDH2 | NM_001289910.1 | c.273G>A | p.Leu91= | synonymous_variant | 4/11 | ||
IDH2 | NM_001290114.2 | c.39G>A | p.Leu13= | synonymous_variant | 2/9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
IDH2 | ENST00000330062.8 | c.429G>A | p.Leu143= | synonymous_variant | 4/11 | 1 | NM_002168.4 | P1 | |
IDH2 | ENST00000540499.2 | c.273G>A | p.Leu91= | synonymous_variant | 4/11 | 2 | |||
IDH2 | ENST00000559482.5 | c.208-190G>A | intron_variant | 5 | |||||
IDH2 | ENST00000560061.1 | c.*54G>A | 3_prime_UTR_variant, NMD_transcript_variant | 2/9 | 2 |
Frequencies
GnomAD3 genomes Cov.: 31
GnomAD3 exomes AF: 0.0000119 AC: 3AN: 251496Hom.: 0 AF XY: 0.0000147 AC XY: 2AN XY: 135922
GnomAD4 exome AF: 0.00000410 AC: 6AN: 1461884Hom.: 0 Cov.: 33 AF XY: 0.00000275 AC XY: 2AN XY: 727244
GnomAD4 genome Cov.: 31
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at