rs755291689
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_StrongBP7
The NM_002168.4(IDH2):c.1194G>T(p.Leu398=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000684 in 1,461,814 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. L398L) 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 -3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
IDH2 | NM_002168.4 | c.1194G>T | p.Leu398= | synonymous_variant | 10/11 | ENST00000330062.8 | |
IDH2 | NM_001289910.1 | c.1038G>T | p.Leu346= | synonymous_variant | 10/11 | ||
IDH2 | NM_001290114.2 | c.804G>T | p.Leu268= | synonymous_variant | 8/9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
IDH2 | ENST00000330062.8 | c.1194G>T | p.Leu398= | synonymous_variant | 10/11 | 1 | NM_002168.4 | P1 | |
IDH2 | ENST00000540499.2 | c.1038G>T | p.Leu346= | synonymous_variant | 10/11 | 2 | |||
IDH2 | ENST00000559482.5 | c.851+108G>T | intron_variant | 5 | |||||
IDH2 | ENST00000560061.1 | c.*819G>T | 3_prime_UTR_variant, NMD_transcript_variant | 8/9 | 2 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.00000398 AC: 1AN: 251418Hom.: 0 AF XY: 0.00000736 AC XY: 1AN XY: 135884
GnomAD4 exome AF: 6.84e-7 AC: 1AN: 1461814Hom.: 0 Cov.: 33 AF XY: 0.00000138 AC XY: 1AN XY: 727206
GnomAD4 genome Cov.: 32
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at