8-39918825-G-T

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NM_002164.6(IDO1):​c.314G>T​(p.Arg105Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000138 in 1,445,904 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: not found (cov: 32)
Exomes 𝑓: 0.0000014 ( 0 hom. )

Consequence

IDO1
NM_002164.6 missense

Scores

1
5
13

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.402
Variant links:
Genes affected
IDO1 (HGNC:6059): (indoleamine 2,3-dioxygenase 1) This gene encodes indoleamine 2,3-dioxygenase (IDO) - a heme enzyme that catalyzes the first and rate-limiting step in tryptophan catabolism to N-formyl-kynurenine. This enzyme acts on multiple tryptophan substrates including D-tryptophan, L-tryptophan, 5-hydroxy-tryptophan, tryptamine, and serotonin. This enzyme is thought to play a role in a variety of pathophysiological processes such as antimicrobial and antitumor defense, neuropathology, immunoregulation, and antioxidant activity. Through its expression in dendritic cells, monocytes, and macrophages this enzyme modulates T-cell behavior by its peri-cellular catabolization of the essential amino acid tryptophan.[provided by RefSeq, Feb 2011]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
IDO1NM_002164.6 linkc.314G>T p.Arg105Ile missense_variant Exon 4 of 10 ENST00000518237.6 NP_002155.1 P14902A0A348GSI3

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
IDO1ENST00000518237.6 linkc.314G>T p.Arg105Ile missense_variant Exon 4 of 10 1 NM_002164.6 ENSP00000430950.1 P14902

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD4 exome
AF:
0.00000138
AC:
2
AN:
1445904
Hom.:
0
Cov.:
30
AF XY:
0.00000278
AC XY:
2
AN XY:
720398
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
9.10e-7
Gnomad4 OTH exome
AF:
0.0000167
GnomAD4 genome
Cov.:
32
Alfa
AF:
0.0000101
Hom.:
0
Bravo
AF:
0.0000113

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.22
BayesDel_addAF
Benign
-0.18
T
BayesDel_noAF
Benign
-0.50
CADD
Benign
21
DANN
Benign
0.96
DEOGEN2
Uncertain
0.52
.;D;D
Eigen
Benign
-0.68
Eigen_PC
Benign
-0.72
FATHMM_MKL
Benign
0.19
N
LIST_S2
Uncertain
0.92
D;.;T
M_CAP
Benign
0.010
T
MetaRNN
Benign
0.23
T;T;T
MetaSVM
Benign
-1.0
T
MutationAssessor
Uncertain
2.2
.;M;M
PrimateAI
Benign
0.21
T
PROVEAN
Pathogenic
-6.0
D;D;D
REVEL
Benign
0.050
Sift
Uncertain
0.0040
D;D;D
Sift4G
Uncertain
0.014
D;D;D
Polyphen
0.41
.;B;B
Vest4
0.36
MutPred
0.58
Loss of MoRF binding (P = 0.0391);Loss of MoRF binding (P = 0.0391);Loss of MoRF binding (P = 0.0391);
MVP
0.26
MPC
0.11
ClinPred
0.97
D
GERP RS
0.94
Varity_R
0.46
gMVP
0.24

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.21
Details are displayed if max score is > 0.2
DS_AL_spliceai
0.21
Position offset: -10

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs12545877; hg19: chr8-39776344; API