chr15-90084859-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_002168.4(IDH2):c.1228G>A(p.Ala410Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000684 in 1,461,798 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 16/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_002168.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
IDH2 | NM_002168.4 | c.1228G>A | p.Ala410Thr | missense_variant | 10/11 | ENST00000330062.8 | |
IDH2 | NM_001289910.1 | c.1072G>A | p.Ala358Thr | missense_variant | 10/11 | ||
IDH2 | NM_001290114.2 | c.838G>A | p.Ala280Thr | missense_variant | 8/9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
IDH2 | ENST00000330062.8 | c.1228G>A | p.Ala410Thr | missense_variant | 10/11 | 1 | NM_002168.4 | P1 | |
IDH2 | ENST00000540499.2 | c.1072G>A | p.Ala358Thr | missense_variant | 10/11 | 2 | |||
IDH2 | ENST00000559482.5 | c.851+142G>A | intron_variant | 5 | |||||
IDH2 | ENST00000560061.1 | c.*853G>A | 3_prime_UTR_variant, NMD_transcript_variant | 8/9 | 2 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.00000398 AC: 1AN: 251410Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135886
GnomAD4 exome AF: 6.84e-7 AC: 1AN: 1461798Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 727206
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 04, 2024 | The c.1228G>A (p.A410T) alteration is located in exon 10 (coding exon 10) of the IDH2 gene. This alteration results from a G to A substitution at nucleotide position 1228, causing the alanine (A) at amino acid position 410 to be replaced by a threonine (T). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at