rs61737002
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong
The NM_002168.4(IDH2):c.993G>T(p.Thr331=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000706 in 1,557,222 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. T331T) 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 -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
IDH2 | NM_002168.4 | c.993G>T | p.Thr331= | synonymous_variant | 8/11 | ENST00000330062.8 | |
IDH2 | NM_001289910.1 | c.837G>T | p.Thr279= | synonymous_variant | 8/11 | ||
IDH2 | NM_001290114.2 | c.603G>T | p.Thr201= | synonymous_variant | 6/9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
IDH2 | ENST00000330062.8 | c.993G>T | p.Thr331= | synonymous_variant | 8/11 | 1 | NM_002168.4 | P1 | |
IDH2 | ENST00000540499.2 | c.837G>T | p.Thr279= | synonymous_variant | 8/11 | 2 | |||
IDH2 | ENST00000559482.5 | c.666G>T | p.Thr222= | synonymous_variant | 6/8 | 5 | |||
IDH2 | ENST00000560061.1 | c.*618G>T | 3_prime_UTR_variant, NMD_transcript_variant | 6/9 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.00000657 AC: 1AN: 152152Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000609 AC: 1AN: 164296Hom.: 0 AF XY: 0.0000115 AC XY: 1AN XY: 86760
GnomAD4 exome AF: 0.00000712 AC: 10AN: 1405070Hom.: 0 Cov.: 32 AF XY: 0.0000101 AC XY: 7AN XY: 693646
GnomAD4 genome ? AF: 0.00000657 AC: 1AN: 152152Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74320
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at