chr8-40005342-A-G
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_194294.5(IDO2):āc.683A>Gā(p.Asp228Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000145 in 1,581,198 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
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.683A>G | p.Asp228Gly | missense_variant | 9/11 | ENST00000502986.4 | |
IDO2 | NM_001395206.1 | c.683A>G | p.Asp228Gly | missense_variant | 8/10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
IDO2 | ENST00000502986.4 | c.683A>G | p.Asp228Gly | missense_variant | 9/11 | 5 | NM_194294.5 | P1 | |
IDO2 | ENST00000343295.8 | n.2971-8223A>G | intron_variant, non_coding_transcript_variant | 2 | |||||
IDO2 | ENST00000418094.1 | n.347-8223A>G | intron_variant, non_coding_transcript_variant | 2 |
Frequencies
GnomAD3 genomes AF: 0.000650 AC: 99AN: 152194Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000196 AC: 47AN: 240372Hom.: 0 AF XY: 0.000238 AC XY: 31AN XY: 130398
GnomAD4 exome AF: 0.0000868 AC: 124AN: 1428886Hom.: 0 Cov.: 27 AF XY: 0.000106 AC XY: 75AN XY: 709204
GnomAD4 genome AF: 0.000689 AC: 105AN: 152312Hom.: 0 Cov.: 33 AF XY: 0.000671 AC XY: 50AN XY: 74478
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 03, 2022 | The c.722A>G (p.D241G) alteration is located in exon 9 (coding exon 9) of the IDO2 gene. This alteration results from a A to G substitution at nucleotide position 722, causing the aspartic acid (D) at amino acid position 241 to be replaced by a glycine (G). 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