rs142816010
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP6BS1BS2
The NM_002168.4(IDH2):c.673G>A(p.Asp225Asn) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000324 in 1,613,648 control chromosomes in the GnomAD database, including 1 homozygotes. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. D225E) has been classified as Uncertain significance.
Frequency
Consequence
NM_002168.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -9 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
IDH2 | NM_002168.4 | c.673G>A | p.Asp225Asn | missense_variant | 5/11 | ENST00000330062.8 | |
IDH2 | NM_001289910.1 | c.517G>A | p.Asp173Asn | missense_variant | 5/11 | ||
IDH2 | NM_001290114.2 | c.283G>A | p.Asp95Asn | missense_variant | 3/9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
IDH2 | ENST00000330062.8 | c.673G>A | p.Asp225Asn | missense_variant | 5/11 | 1 | NM_002168.4 | P1 | |
IDH2 | ENST00000540499.2 | c.517G>A | p.Asp173Asn | missense_variant | 5/11 | 2 | |||
IDH2 | ENST00000559482.5 | c.346G>A | p.Asp116Asn | missense_variant | 3/8 | 5 | |||
IDH2 | ENST00000560061.1 | c.*298G>A | 3_prime_UTR_variant, NMD_transcript_variant | 3/9 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.000342 AC: 52AN: 152226Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.000291 AC: 73AN: 250944Hom.: 0 AF XY: 0.000317 AC XY: 43AN XY: 135710
GnomAD4 exome AF: 0.000322 AC: 471AN: 1461304Hom.: 1 Cov.: 33 AF XY: 0.000314 AC XY: 228AN XY: 726976
GnomAD4 genome ? AF: 0.000341 AC: 52AN: 152344Hom.: 0 Cov.: 31 AF XY: 0.000282 AC XY: 21AN XY: 74498
ClinVar
Submissions by phenotype
not provided Uncertain:2
Uncertain significance, criteria provided, single submitter | clinical testing | GeneDx | May 11, 2021 | In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; Has not been previously published as pathogenic or benign to our knowledge - |
Uncertain significance, criteria provided, single submitter | clinical testing | Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics | Nov 22, 2016 | - - |
Enchondromatosis Uncertain:1
Uncertain significance, criteria provided, single submitter | research | Baylor-Hopkins Center for Mendelian Genomics, Johns Hopkins University School of Medicine | - | - - |
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Mar 06, 2015 | - - |
D-2-hydroxyglutaric aciduria 2 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jul 09, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at