rs4445211

chr8-40014064-G-Cchr8-40014064-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_194294.5(IDO2):c.868+351G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.383 in 152,038 control chromosomes in the GnomAD database, including 11,583 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 (11583 hom., cov: 31)
• Consequence: IDO2 NM_194294.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.139

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.506 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
IDO2	NM_194294.5	c.868+351G>C		intron_variant		ENST00000502986.4
IDO2	NM_001395206.1	c.868+351G>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
IDO2	ENST00000502986.4	c.868+351G>C		intron_variant		5	NM_194294.5	P1
IDO2	ENST00000343295.8	n.3119+351G>C		intron_variant, non_coding_transcript_variant		2
IDO2	ENST00000418094.1	n.495+351G>C		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.383 AC: 58225 AN: 151922 Hom.: 11568 Cov.: 31

Gnomad AFR AF: 0.400

Gnomad AMI AF: 0.486

Gnomad AMR AF: 0.515

Gnomad ASJ AF: 0.314

Gnomad EAS AF: 0.381

Gnomad SAS AF: 0.302

Gnomad FIN AF: 0.350

Gnomad MID AF: 0.342

Gnomad NFE AF: 0.357

Gnomad OTH AF: 0.392

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.383 AC: 58271 AN: 152038 Hom.: 11583 Cov.: 31 AF XY: 0.383 AC XY: 28492 AN XY: 74328

Gnomad4 AFR AF: 0.400

Gnomad4 AMR AF: 0.515

Gnomad4 ASJ AF: 0.314

Gnomad4 EAS AF: 0.380

Gnomad4 SAS AF: 0.300

Gnomad4 FIN AF: 0.350

Gnomad4 NFE AF: 0.357

Gnomad4 OTH AF: 0.394

Alfa AF: 0.231 Hom.: 506

Bravo AF: 0.404

Asia WGS AF: 0.358 AC: 1242 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
Cadd	Benign	1.3
Dann	Benign	0.48

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

Other links and lift over

dbSNP: rs4445211; hg19: chr8-39871583;