8-39963700-C-G
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_194294.5(IDO2):c.192C>G(p.Asp64Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000129 in 1,591,810 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_194294.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
IDO2 | NM_194294.5 | c.192C>G | p.Asp64Glu | missense_variant | 3/11 | ENST00000502986.4 | |
IDO2 | NM_001395206.1 | c.192C>G | p.Asp64Glu | missense_variant | 2/10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
IDO2 | ENST00000502986.4 | c.192C>G | p.Asp64Glu | missense_variant | 3/11 | 5 | NM_194294.5 | P1 | |
ENST00000517623.1 | n.255+23678G>C | intron_variant, non_coding_transcript_variant | 4 | ||||||
IDO2 | ENST00000343295.8 | n.814C>G | non_coding_transcript_exon_variant | 3/11 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.000690 AC: 105AN: 152148Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000153 AC: 37AN: 242488Hom.: 0 AF XY: 0.000145 AC XY: 19AN XY: 131400
GnomAD4 exome AF: 0.0000702 AC: 101AN: 1439544Hom.: 0 Cov.: 25 AF XY: 0.0000572 AC XY: 41AN XY: 716950
GnomAD4 genome ? AF: 0.000683 AC: 104AN: 152266Hom.: 0 Cov.: 33 AF XY: 0.000672 AC XY: 50AN XY: 74448
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 03, 2022 | The c.231C>G (p.D77E) alteration is located in exon 3 (coding exon 3) of the IDO2 gene. This alteration results from a C to G substitution at nucleotide position 231, causing the aspartic acid (D) at amino acid position 77 to be replaced by a glutamic acid (E). 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