rs8178561

Positions:

• chr21-33296492-G-A

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The NM_000628.5(IL10RB):​c.*135G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0582 in 850,424 control chromosomes in the GnomAD database, including 1,893 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.079 (642 hom., cov: 32)
  • Exomes 𝑓: 0.054 (1251 hom.)
• Consequence: IL10RB NM_000628.5 3_prime_UTR
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.190

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]

IFNAR2-IL10RB (HGNC:):

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BP6: Variant 21-33296492-G-A is Benign according to our data. Variant chr21-33296492-G-A is described in ClinVar as [Benign]. Clinvar id is 339699.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.138 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
IL10RB	NM_000628.5	c.*135G>A		3_prime_UTR_variant	7/7	ENST00000290200.7
IFNAR2-IL10RB	NM_001414505.1	c.*135G>A		3_prime_UTR_variant	13/13

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
IL10RB	ENST00000290200.7	c.*135G>A		3_prime_UTR_variant	7/7	1	NM_000628.5	P2
IL10RB	ENST00000609556.3	c.804+8231G>A		intron_variant		5		A2
IL10RB	ENST00000637650.2	c.804+8231G>A		intron_variant		5		A2
IL10RB	ENST00000493295.5	n.1530G>A		non_coding_transcript_exon_variant	6/6	2

Frequencies

GnomAD3 genomes AF: 0.0788 AC: 11982 AN: 152092 Hom.: 635 Cov.: 32

Gnomad AFR AF: 0.141

Gnomad AMI AF: 0.0274

Gnomad AMR AF: 0.0576

Gnomad ASJ AF: 0.0868

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00911

Gnomad FIN AF: 0.0538

Gnomad MID AF: 0.0886

Gnomad NFE AF: 0.0609

Gnomad OTH AF: 0.0746

GnomAD3 exomes AF: 0.0483 AC: 6733 AN: 139398 Hom.: 244 AF XY: 0.0452 AC XY: 3421 AN XY: 75722

Gnomad AFR exome AF: 0.147

Gnomad AMR exome AF: 0.0369

Gnomad ASJ exome AF: 0.0896

Gnomad EAS exome AF: 0.00115

Gnomad SAS exome AF: 0.0113

Gnomad FIN exome AF: 0.0510

Gnomad NFE exome AF: 0.0597

Gnomad OTH exome AF: 0.0561

GnomAD4 exome AF: 0.0536 AC: 37454 AN: 698214 Hom.: 1251 Cov.: 9 AF XY: 0.0508 AC XY: 18776 AN XY: 369298

Gnomad4 AFR exome AF: 0.142

Gnomad4 AMR exome AF: 0.0382

Gnomad4 ASJ exome AF: 0.0903

Gnomad4 EAS exome AF: 0.000579

Gnomad4 SAS exome AF: 0.0118

Gnomad4 FIN exome AF: 0.0479

Gnomad4 NFE exome AF: 0.0589

Gnomad4 OTH exome AF: 0.0652

GnomAD4 genome AF: 0.0789 AC: 12015 AN: 152210 Hom.: 642 Cov.: 32 AF XY: 0.0776 AC XY: 5772 AN XY: 74418

Gnomad4 AFR AF: 0.141

Gnomad4 AMR AF: 0.0575

Gnomad4 ASJ AF: 0.0868

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00891

Gnomad4 FIN AF: 0.0538

Gnomad4 NFE AF: 0.0609

Gnomad4 OTH AF: 0.0771

Alfa AF: 0.0640 Hom.: 354

Bravo AF: 0.0816

Asia WGS AF: 0.0360 AC: 125 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

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. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.8
DANN	Benign	0.28
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

Other links and lift over

dbSNP: rs8178561; hg19: chr21-34668797;