rs35212142
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBS1BS2
The NM_194294.5(IDO2):c.715T>A(p.Ser239Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0303 in 1,561,968 control chromosomes in the GnomAD database, including 892 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 0.024 ( 69 hom., cov: 33)
Exomes 𝑓: 0.031 ( 823 hom. )
Consequence
IDO2
NM_194294.5 missense
NM_194294.5 missense
Scores
9
8
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 3.45
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 -12 ACMG points.
BP4
?
Computational evidence support a benign effect (MetaRNN=0.015613109).
BS1
?
Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0238 (3620/152348) while in subpopulation NFE AF= 0.0375 (2549/68034). AF 95% confidence interval is 0.0363. There are 69 homozygotes in gnomad4. There are 1715 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd4 at 69 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
IDO2 | NM_194294.5 | c.715T>A | p.Ser239Thr | missense_variant | 9/11 | ENST00000502986.4 | |
IDO2 | NM_001395206.1 | c.715T>A | p.Ser239Thr | missense_variant | 8/10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
IDO2 | ENST00000502986.4 | c.715T>A | p.Ser239Thr | missense_variant | 9/11 | 5 | NM_194294.5 | P1 | |
IDO2 | ENST00000343295.8 | n.2971-8191T>A | intron_variant, non_coding_transcript_variant | 2 | |||||
IDO2 | ENST00000418094.1 | n.347-8191T>A | intron_variant, non_coding_transcript_variant | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0238 AC: 3620AN: 152230Hom.: 69 Cov.: 33
GnomAD3 genomes
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GnomAD3 exomes AF: 0.0203 AC: 4824AN: 238208Hom.: 88 AF XY: 0.0203 AC XY: 2627AN XY: 129262
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GnomAD4 exome AF: 0.0310 AC: 43720AN: 1409620Hom.: 823 Cov.: 26 AF XY: 0.0306 AC XY: 21365AN XY: 699254
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GnomAD4 genome ? AF: 0.0238 AC: 3620AN: 152348Hom.: 69 Cov.: 33 AF XY: 0.0230 AC XY: 1715AN XY: 74494
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132
ALSPAC
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151
ESP6500AA
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23
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254
ExAC
?
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2658
Asia WGS
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3476
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Uncertain
DANN
Uncertain
DEOGEN2
Benign
T;.
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Uncertain
D
LIST_S2
Uncertain
D;D
MetaRNN
Benign
T;T
MetaSVM
Benign
T
MutationTaster
Benign
D;D
PrimateAI
Benign
T
PROVEAN
Uncertain
D;D
REVEL
Uncertain
Sift
Uncertain
D;D
Sift4G
Uncertain
D;D
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