8-39963651-A-G
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_194294.5(IDO2):c.143A>G(p.Asn48Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000031 in 1,612,662 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 Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
IDO2 | NM_194294.5 | c.143A>G | p.Asn48Ser | missense_variant | 3/11 | ENST00000502986.4 | |
IDO2 | NM_001395206.1 | c.143A>G | p.Asn48Ser | missense_variant | 2/10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
IDO2 | ENST00000502986.4 | c.143A>G | p.Asn48Ser | missense_variant | 3/11 | 5 | NM_194294.5 | P1 | |
ENST00000517623.1 | n.255+23727T>C | intron_variant, non_coding_transcript_variant | 4 | ||||||
IDO2 | ENST00000343295.8 | n.765A>G | non_coding_transcript_exon_variant | 3/11 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.00000657 AC: 1AN: 152206Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000121 AC: 3AN: 247894Hom.: 0 AF XY: 0.0000149 AC XY: 2AN XY: 134448
GnomAD4 exome AF: 0.00000274 AC: 4AN: 1460456Hom.: 0 Cov.: 28 AF XY: 0.00000275 AC XY: 2AN XY: 726472
GnomAD4 genome ? AF: 0.00000657 AC: 1AN: 152206Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 74372
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 04, 2023 | The c.182A>G (p.N61S) alteration is located in exon 3 (coding exon 3) of the IDO2 gene. This alteration results from a A to G substitution at nucleotide position 182, causing the asparagine (N) at amino acid position 61 to be replaced by a serine (S). 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