rs142801125
Variant summary
Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PM2PP3_Strong
The NM_005896.4(IDH1):āc.659A>Gā(p.Asp220Gly) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000682 in 1,613,942 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as not provided (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. D220N) has been classified as Uncertain significance.
Frequency
Consequence
NM_005896.4 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_pathogenic. Variant got 6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
IDH1 | NM_005896.4 | c.659A>G | p.Asp220Gly | missense_variant | 6/10 | ENST00000345146.7 | |
IDH1 | NM_001282386.1 | c.659A>G | p.Asp220Gly | missense_variant | 6/10 | ||
IDH1 | NM_001282387.1 | c.659A>G | p.Asp220Gly | missense_variant | 6/10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
IDH1 | ENST00000345146.7 | c.659A>G | p.Asp220Gly | missense_variant | 6/10 | 1 | NM_005896.4 | P1 | |
IDH1 | ENST00000415913.5 | c.659A>G | p.Asp220Gly | missense_variant | 6/10 | 1 | P1 | ||
IDH1 | ENST00000446179.5 | c.659A>G | p.Asp220Gly | missense_variant | 6/10 | 1 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000460 AC: 7AN: 152194Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000597 AC: 15AN: 251368Hom.: 0 AF XY: 0.0000810 AC XY: 11AN XY: 135868
GnomAD4 exome AF: 0.0000705 AC: 103AN: 1461630Hom.: 0 Cov.: 30 AF XY: 0.0000825 AC XY: 60AN XY: 727134
GnomAD4 genome AF: 0.0000460 AC: 7AN: 152312Hom.: 0 Cov.: 32 AF XY: 0.0000403 AC XY: 3AN XY: 74474
ClinVar
Submissions by phenotype
not specified Other:1
not provided, no classification provided | reference population | ITMI | Sep 19, 2013 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at