NM_002164.6:c.857-28G>A
Variant names:
Variant summary
Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_002164.6(IDO1):c.857-28G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.397 in 1,419,442 control chromosomes in the GnomAD database, including 114,592 homozygotes. 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: 𝑓 0.38 ( 11218 hom., cov: 30)
Exomes 𝑓: 0.40 ( 103374 hom. )
Consequence
IDO1
NM_002164.6 intron
NM_002164.6 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -2.57
Publications
30 publications found
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 was made for transcript
Our verdict: Benign. The variant received -12 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.9).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.539 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
IDO1 | NM_002164.6 | c.857-28G>A | intron_variant | Intron 9 of 9 | ENST00000518237.6 | NP_002155.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.378 AC: 57382AN: 151692Hom.: 11218 Cov.: 30 show subpopulations
GnomAD3 genomes
AF:
AC:
57382
AN:
151692
Hom.:
Cov.:
30
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD2 exomes AF: 0.404 AC: 41684AN: 103296 AF XY: 0.412 show subpopulations
GnomAD2 exomes
AF:
AC:
41684
AN:
103296
AF XY:
Gnomad AFR exome
AF:
Gnomad AMR exome
AF:
Gnomad ASJ exome
AF:
Gnomad EAS exome
AF:
Gnomad FIN exome
AF:
Gnomad NFE exome
AF:
Gnomad OTH exome
AF:
GnomAD4 exome AF: 0.399 AC: 506283AN: 1267630Hom.: 103374 Cov.: 19 AF XY: 0.403 AC XY: 249376AN XY: 618646 show subpopulations
GnomAD4 exome
AF:
AC:
506283
AN:
1267630
Hom.:
Cov.:
19
AF XY:
AC XY:
249376
AN XY:
618646
show subpopulations
African (AFR)
AF:
AC:
9459
AN:
28142
American (AMR)
AF:
AC:
6928
AN:
22162
Ashkenazi Jewish (ASJ)
AF:
AC:
9099
AN:
18898
East Asian (EAS)
AF:
AC:
19791
AN:
35924
South Asian (SAS)
AF:
AC:
33273
AN:
61822
European-Finnish (FIN)
AF:
AC:
18404
AN:
45640
Middle Eastern (MID)
AF:
AC:
2940
AN:
5144
European-Non Finnish (NFE)
AF:
AC:
384432
AN:
996986
Other (OTH)
AF:
AC:
21957
AN:
52912
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.502
Heterozygous variant carriers
0
14575
29150
43725
58300
72875
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Exome Het
Exome Hom
Variant carriers
0
12448
24896
37344
49792
62240
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
GnomAD4 genome AF: 0.378 AC: 57419AN: 151812Hom.: 11218 Cov.: 30 AF XY: 0.381 AC XY: 28275AN XY: 74184 show subpopulations
GnomAD4 genome
AF:
AC:
57419
AN:
151812
Hom.:
Cov.:
30
AF XY:
AC XY:
28275
AN XY:
74184
show subpopulations
African (AFR)
AF:
AC:
13030
AN:
41366
American (AMR)
AF:
AC:
5236
AN:
15268
Ashkenazi Jewish (ASJ)
AF:
AC:
1694
AN:
3464
East Asian (EAS)
AF:
AC:
2863
AN:
5146
South Asian (SAS)
AF:
AC:
2619
AN:
4798
European-Finnish (FIN)
AF:
AC:
3998
AN:
10532
Middle Eastern (MID)
AF:
AC:
145
AN:
294
European-Non Finnish (NFE)
AF:
AC:
26653
AN:
67924
Other (OTH)
AF:
AC:
829
AN:
2108
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.503
Heterozygous variant carriers
0
1774
3548
5323
7097
8871
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Genome Het
Genome Hom
Variant carriers
0
574
1148
1722
2296
2870
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
1786
AN:
3478
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.