Variant chr21-33266554-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The NM_000628.5(IL10RB):c.49+40G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.69 in 1,535,164 control chromosomes in the GnomAD database, including 368,399 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.64 ( 31879 hom., cov: 32)

Exomes 𝑓: 0.70 ( 336520 hom. )

Consequence

IL10RB
NM_000628.5 intron

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.123

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 -14 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.85).

BP6

Variant 21-33266554-G-A is Benign according to our data. Variant chr21-33266554-G-A is described in ClinVar as [Benign]. Clinvar id is 2628110.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.747 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
IL10RB	NM_000628.5 linkuse as main transcript	c.49+40G>A		intron_variant		ENST00000290200.7
IFNAR2-IL10RB	NM_001414505.1 linkuse as main transcript	c.710-1840G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
IL10RB	ENST00000290200.7 linkuse as main transcript	c.49+40G>A		intron_variant		1	NM_000628.5	P2

Frequencies

GnomAD3 genomes

AF:

0.638

AC:

96878

AN:

151948

Hom.:

31871

Cov.:

show subpopulations

Gnomad AFR

AF:

0.468

Gnomad AMI

AF:

0.468

Gnomad AMR

AF:

0.624

Gnomad ASJ

AF:

0.728

Gnomad EAS

AF:

0.767

Gnomad SAS

AF:

0.666

Gnomad FIN

AF:

0.733

Gnomad MID

AF:

0.585

Gnomad NFE

AF:

0.715

Gnomad OTH

AF:

0.652

GnomAD3 exomes

AF:

0.682

AC:

94397

AN:

138502

Hom.:

32711

AF XY:

0.687

AC XY:

50927

AN XY:

74170

show subpopulations

Gnomad AFR exome

AF:

0.461

Gnomad AMR exome

AF:

0.622

Gnomad ASJ exome

AF:

0.740

Gnomad EAS exome

AF:

0.767

Gnomad SAS exome

AF:

0.663

Gnomad FIN exome

AF:

0.730

Gnomad NFE exome

AF:

0.716

Gnomad OTH exome

AF:

0.673

GnomAD4 exome

AF:

0.696

AC:

962292

AN:

1383098

Hom.:

336520

Cov.:

AF XY:

0.697

AC XY:

475993

AN XY:

682854

show subpopulations

Gnomad4 AFR exome

AF:

0.464

Gnomad4 AMR exome

AF:

0.624

Gnomad4 ASJ exome

AF:

0.741

Gnomad4 EAS exome

AF:

0.753

Gnomad4 SAS exome

AF:

0.665

Gnomad4 FIN exome

AF:

0.731

Gnomad4 NFE exome

AF:

0.704

Gnomad4 OTH exome

AF:

0.689

GnomAD4 genome

AF:

0.637

AC:

96927

AN:

152066

Hom.:

31879

Cov.:

AF XY:

0.640

AC XY:

47622

AN XY:

74354

show subpopulations

Gnomad4 AFR

AF:

0.468

Gnomad4 AMR

AF:

0.625

Gnomad4 ASJ

AF:

0.728

Gnomad4 EAS

AF:

0.767

Gnomad4 SAS

AF:

0.666

Gnomad4 FIN

AF:

0.733

Gnomad4 NFE

AF:

0.715

Gnomad4 OTH

AF:

0.650

Alfa

AF:

0.677

Hom.:

8935

Bravo

AF:

0.624

Asia WGS

AF:

0.679

AC:

2360

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

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 82% of patients studied by a panel of primary immunodeficiencies. Number of patients: 79. Only high quality variants are reported. -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.85

CADD

Benign

8.7

DANN

Benign

0.85

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