rs3171425

Positions:

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The ENST00000290200.7(IL10RB):c.*85A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.594 in 1,352,454 control chromosomes in the GnomAD database, including 241,560 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.54 ( 23192 hom., cov: 31)

Exomes 𝑓: 0.60 ( 218368 hom. )

Consequence

IL10RB
ENST00000290200.7 3_prime_UTR

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:3

Conservation

PhyloP100: -2.29

Variant links:

Genes affected

IL10RB (HGNC:5965): (interleukin 10 receptor subunit beta) The protein encoded by this gene belongs to the cytokine receptor family. It is an accessory chain essential for the active interleukin 10 receptor complex. Coexpression of this and IL10RA proteins has been shown to be required for IL10-induced signal transduction. This gene and three other interferon receptor genes, IFAR2, IFNAR1, and IFNGR2, form a class II cytokine receptor gene cluster located in a small region on chromosome 21. [provided by RefSeq, Jul 2008]

IL10RB links:

IFNAR2-IL10RB (HGNC:):

IFNAR2-IL10RB links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.92).

BP6

Variant 21-33296442-A-G is Benign according to our data. Variant chr21-33296442-A-G is described in ClinVar as [Benign]. Clinvar id is 339698.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.73 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
IL10RB	NM_000628.5 linkuse as main transcript	c.*85A>G		3_prime_UTR_variant	7/7	ENST00000290200.7	NP_000619.3
IFNAR2-IL10RB	NM_001414505.1 linkuse as main transcript	c.*85A>G		3_prime_UTR_variant	13/13		NP_001401434.1

Ensembl

Gene	Transcript	HGVSc	Effect	#exon/exons	TSL	MANE	Protein	Appris
IL10RB	ENST00000290200.7 linkuse as main transcript	c.*85A>G	3_prime_UTR_variant	7/7	1	NM_000628.5	ENSP00000290200	P2
IL10RB	ENST00000609556.3 linkuse as main transcript	c.804+8181A>G	intron_variant		5		ENSP00000489965	A2
IL10RB	ENST00000637650.2 linkuse as main transcript	c.804+8181A>G	intron_variant		5		ENSP00000489716	A2
IL10RB	ENST00000493295.5 linkuse as main transcript	n.1480A>G	non_coding_transcript_exon_variant	6/6	2

Frequencies

GnomAD3 genomes

AF:

0.539

AC:

81818

AN:

151914

Hom.:

23200

Cov.:

show subpopulations

Gnomad AFR

AF:

0.359

Gnomad AMI

AF:

0.638

Gnomad AMR

AF:

0.583

Gnomad ASJ

AF:

0.475

Gnomad EAS

AF:

0.751

Gnomad SAS

AF:

0.672

Gnomad FIN

AF:

0.655

Gnomad MID

AF:

0.598

Gnomad NFE

AF:

0.596

Gnomad OTH

AF:

0.557

GnomAD3 exomes

AF:

0.603

AC:

112453

AN:

186518

Hom.:

34253

AF XY:

0.606

AC XY:

61961

AN XY:

102170

show subpopulations

Gnomad AFR exome

AF:

0.358

Gnomad AMR exome

AF:

0.611

Gnomad ASJ exome

AF:

0.477

Gnomad EAS exome

AF:

0.745

Gnomad SAS exome

AF:

0.666

Gnomad FIN exome

AF:

0.665

Gnomad NFE exome

AF:

0.595

Gnomad OTH exome

AF:

0.606

GnomAD4 exome

AF:

0.601

AC:

721012

AN:

1200422

Hom.:

218368

Cov.:

AF XY:

0.603

AC XY:

365803

AN XY:

606570

show subpopulations

Gnomad4 AFR exome

AF:

0.350

Gnomad4 AMR exome

AF:

0.602

Gnomad4 ASJ exome

AF:

0.470

Gnomad4 EAS exome

AF:

0.763

Gnomad4 SAS exome

AF:

0.661

Gnomad4 FIN exome

AF:

0.652

Gnomad4 NFE exome

AF:

0.598

Gnomad4 OTH exome

AF:

0.597

GnomAD4 genome

AF:

0.538

AC:

81819

AN:

152032

Hom.:

23192

Cov.:

AF XY:

0.544

AC XY:

40384

AN XY:

74302

show subpopulations

Gnomad4 AFR

AF:

0.358

Gnomad4 AMR

AF:

0.583

Gnomad4 ASJ

AF:

0.475

Gnomad4 EAS

AF:

0.750

Gnomad4 SAS

AF:

0.671

Gnomad4 FIN

AF:

0.655

Gnomad4 NFE

AF:

0.596

Gnomad4 OTH

AF:

0.558

Alfa

AF:

0.574

Hom.:

26104

Bravo

AF:

0.525

Asia WGS

AF:

0.708

AC:

2463

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:3

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:1

Benign, criteria provided, single submitter

clinical testing

Unidad de Genómica Garrahan, Hospital de Pediatría Garrahan

Nov 12, 2023

This variant is classified as Benign based on local population frequency. This variant was detected in 76% of patients studied by a panel of primary immunodeficiencies. Number of patients: 73. Only high quality variants are reported. -

Inflammatory bowel disease 25

Benign:1

Benign, criteria provided, single submitter

clinical testing

Illumina Laboratory Services, Illumina

Jan 13, 2018

This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. -

not provided

Benign:1

Benign, criteria provided, single submitter

not provided

Breakthrough Genomics, Breakthrough Genomics

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.92

CADD

Benign

0.059

DANN

Benign

0.45

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

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