8-39925338-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_002164.6(IDO1):c.823G>A(p.Val275Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000756 in 1,612,962 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_002164.6 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 | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
IDO1 | NM_002164.6 | c.823G>A | p.Val275Ile | missense_variant | 9/10 | ENST00000518237.6 | NP_002155.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
IDO1 | ENST00000518237.6 | c.823G>A | p.Val275Ile | missense_variant | 9/10 | 1 | NM_002164.6 | ENSP00000430950 | P1 | |
ENST00000517623.1 | n.256-21317C>T | intron_variant, non_coding_transcript_variant | 4 |
Frequencies
GnomAD3 genomes AF: 0.000112 AC: 17AN: 152182Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000133 AC: 33AN: 247692Hom.: 0 AF XY: 0.000164 AC XY: 22AN XY: 134436
GnomAD4 exome AF: 0.0000719 AC: 105AN: 1460662Hom.: 0 Cov.: 31 AF XY: 0.0000743 AC XY: 54AN XY: 726586
GnomAD4 genome AF: 0.000112 AC: 17AN: 152300Hom.: 0 Cov.: 32 AF XY: 0.0000806 AC XY: 6AN XY: 74472
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | May 31, 2023 | The c.823G>A (p.V275I) alteration is located in exon 9 (coding exon 9) of the IDO1 gene. This alteration results from a G to A substitution at nucleotide position 823, causing the valine (V) at amino acid position 275 to be replaced by an isoleucine (I). 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