Variant rs4503083 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP6_Very_StrongBA1

The NM_194294.5(IDO2):c.1038T>A(p.Tyr346*) variant causes a stop gained change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.207 in 1,613,680 control chromosomes in the GnomAD database, including 35,935 homozygotes. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.20 ( 3180 hom., cov: 32)

Exomes 𝑓: 0.21 ( 32755 hom. )

Consequence

IDO2
NM_194294.5 stop_gained

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 0.108

Variant links:

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]

IDO2 links:

IDO2 (HGNC:):

IDO2 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -16 ACMG points.

BP6

Variant 8-40015416-T-A is Benign according to our data. Variant chr8-40015416-T-A is described in ClinVar as [Benign]. Clinvar id is 1229251.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.347 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
IDO2	NM_194294.5 linkuse as main transcript	c.1038T>A	p.Tyr346*	stop_gained	11/11	ENST00000502986.4	NP_919270.3	Q6ZQW0
IDO2	NM_001395206.1 linkuse as main transcript	c.1038T>A	p.Tyr346*	stop_gained	10/10		NP_001382135.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	UniProt
IDO2	ENST00000502986.4 linkuse as main transcript	c.1038T>A	p.Tyr346*	stop_gained	11/11	5	NM_194294.5	ENSP00000443432.2	Q6ZQW0
IDO2	ENST00000343295.8 linkuse as main transcript	n.3289T>A		non_coding_transcript_exon_variant	11/11	2
IDO2	ENST00000418094.1 linkuse as main transcript	n.665T>A		non_coding_transcript_exon_variant	4/4	2

Frequencies

GnomAD3 genomes

AF:

0.197

AC:

29890

AN:

151990

Hom.:

3179

Cov.:

show subpopulations

Gnomad AFR

AF:

0.125

Gnomad AMI

AF:

0.378

Gnomad AMR

AF:

0.265

Gnomad ASJ

AF:

0.165

Gnomad EAS

AF:

0.362

Gnomad SAS

AF:

0.228

Gnomad FIN

AF:

0.199

Gnomad MID

AF:

0.199

Gnomad NFE

AF:

0.209

Gnomad OTH

AF:

0.210

GnomAD3 exomes

AF:

0.227

AC:

56546

AN:

248808

Hom.:

6915

AF XY:

0.227

AC XY:

30665

AN XY:

134968

show subpopulations

Gnomad AFR exome

AF:

0.122

Gnomad AMR exome

AF:

0.280

Gnomad ASJ exome

AF:

0.159

Gnomad EAS exome

AF:

0.378

Gnomad SAS exome

AF:

0.231

Gnomad FIN exome

AF:

0.207

Gnomad NFE exome

AF:

0.211

Gnomad OTH exome

AF:

0.209

GnomAD4 exome

AF:

0.208

AC:

304115

AN:

1461576

Hom.:

32755

Cov.:

AF XY:

0.209

AC XY:

152000

AN XY:

727050

show subpopulations

Gnomad4 AFR exome

AF:

0.124

Gnomad4 AMR exome

AF:

0.278

Gnomad4 ASJ exome

AF:

0.160

Gnomad4 EAS exome

AF:

0.374

Gnomad4 SAS exome

AF:

0.231

Gnomad4 FIN exome

AF:

0.205

Gnomad4 NFE exome

AF:

0.201

Gnomad4 OTH exome

AF:

0.204

GnomAD4 genome

AF:

0.197

AC:

29895

AN:

152104

Hom.:

3180

Cov.:

AF XY:

0.200

AC XY:

14865

AN XY:

74360

show subpopulations

Gnomad4 AFR

AF:

0.125

Gnomad4 AMR

AF:

0.265

Gnomad4 ASJ

AF:

0.165

Gnomad4 EAS

AF:

0.361

Gnomad4 SAS

AF:

0.227

Gnomad4 FIN

AF:

0.199

Gnomad4 NFE

AF:

0.209

Gnomad4 OTH

AF:

0.214

Alfa

AF:

0.199

Hom.:

987

Bravo

AF:

0.200

TwinsUK

AF:

0.201

AC:

744

ALSPAC

AF:

0.213

AC:

821

ESP6500AA

AF:

0.110

AC:

458

ESP6500EA

AF:

0.207

AC:

1743

ExAC

AF:

0.225

AC:

27248

Asia WGS

AF:

0.279

AC:

969

AN:

3478

EpiCase

AF:

0.207

EpiControl

AF:

0.213

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Jan 10, 2019	This variant is associated with the following publications: (PMID: 25541686, 17671174) -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_addAF

Uncertain

0.15

BayesDel_noAF

Pathogenic

0.59

CADD

Pathogenic

DANN

Uncertain

0.99

Eigen

Uncertain

0.36

Eigen_PC

Benign

0.11

FATHMM_MKL

Uncertain

0.86

Vest4

0.89

GERP RS

-2.2

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over