rs4736794
Positions:
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_194294.5(IDO2):āc.379A>Gā(p.Ile127Val) variant causes a missense change. The variant allele was found at a frequency of 0.103 in 1,610,022 control chromosomes in the GnomAD database, including 11,305 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ).
Frequency
Genomes: š 0.10 ( 1160 hom., cov: 32)
Exomes š: 0.10 ( 10145 hom. )
Consequence
IDO2
NM_194294.5 missense
NM_194294.5 missense
Scores
1
3
13
Clinical Significance
Conservation
PhyloP100: 5.11
Genes affected
IDO2 (HGNC:27269): (indoleamine 2,3-dioxygenase 2) Along with the enzymes encoded by the INDO (MIM 147435) and TDO2 (MIM 191070) genes, the enzyme encoded by the INDOL1 gene metabolizes tryptophan in the kynurenine pathway (Ball et al., 2007 [PubMed 17499941]).[supplied by OMIM, Feb 2011]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -14 ACMG points.
BP4
?
Computational evidence support a benign effect (MetaRNN=0.00180915).
BP6
?
Variant 8-39982715-A-G is Benign according to our data. Variant chr8-39982715-A-G is described in ClinVar as [Benign]. Clinvar id is 1265377.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.327 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
IDO2 | NM_194294.5 | c.379A>G | p.Ile127Val | missense_variant | 5/11 | ENST00000502986.4 | |
IDO2 | NM_001395206.1 | c.379A>G | p.Ile127Val | missense_variant | 4/10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
IDO2 | ENST00000502986.4 | c.379A>G | p.Ile127Val | missense_variant | 5/11 | 5 | NM_194294.5 | P1 | |
ENST00000517623.1 | n.255+4663T>C | intron_variant, non_coding_transcript_variant | 4 | ||||||
IDO2 | ENST00000343295.8 | n.1001A>G | non_coding_transcript_exon_variant | 5/11 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.100 AC: 15217AN: 152094Hom.: 1162 Cov.: 32
GnomAD3 genomes
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GnomAD3 exomes AF: 0.140 AC: 34332AN: 244976Hom.: 3273 AF XY: 0.142 AC XY: 18814AN XY: 132696
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GnomAD4 exome AF: 0.104 AC: 151055AN: 1457810Hom.: 10145 Cov.: 30 AF XY: 0.107 AC XY: 77378AN XY: 724884
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GnomAD4 genome ? AF: 0.100 AC: 15220AN: 152212Hom.: 1160 Cov.: 32 AF XY: 0.106 AC XY: 7918AN XY: 74426
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286
ALSPAC
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367
ESP6500AA
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115
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780
ExAC
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16459
Asia WGS
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900
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3478
ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Apr 30, 2021 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Benign
DANN
Pathogenic
DEOGEN2
Benign
T;.
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Uncertain
D
LIST_S2
Benign
T;T
MetaRNN
Benign
T;T
MetaSVM
Benign
T
MutationTaster
Benign
P;P
PrimateAI
Benign
T
PROVEAN
Benign
N;N
REVEL
Benign
Sift
Benign
D;D
Sift4G
Benign
T;T
Vest4
MPC
ClinPred
T
GERP RS
Varity_R
gMVP
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at