Variant rs10903022 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BA1

The NM_021258.4(IL22RA1):c.135G>A(p.Pro45=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.399 in 1,613,546 control chromosomes in the GnomAD database, including 133,757 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.37 ( 11319 hom., cov: 32)

Exomes 𝑓: 0.40 ( 122438 hom. )

Consequence

IL22RA1
NM_021258.4 synonymous

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -2.57

Variant links:

Genes affected

IL22RA1 (HGNC:13700): (interleukin 22 receptor subunit alpha 1) The protein encoded by this gene belongs to the class II cytokine receptor family, and has been shown to be a receptor for interleukin 22 (IL22). IL22 receptor is a protein complex that consists of this protein and interleukin 10 receptor, beta (IL10BR/CRFB4), a subunit also shared by the receptor complex for interleukin 10 (IL10). This gene and interleukin 28 receptor, alpha (IL28RA) form a cytokine receptor gene cluster in the chromosomal region 1p36. [provided by RefSeq, Jul 2008]

IL22RA1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -15 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.73).

BP6

Variant 1-24138623-C-T is Benign according to our data. Variant chr1-24138623-C-T is described in ClinVar as [Benign]. Clinvar id is 2688368.Status of the report is criteria_provided_single_submitter, 1 stars.

BP7

Synonymous conserved (PhyloP=-2.57 with no splicing effect.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.725 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
IL22RA1	NM_021258.4 linkuse as main transcript	c.135G>A	p.Pro45=	synonymous_variant	2/7	ENST00000270800.2	NP_067081.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
IL22RA1	ENST00000270800.2 linkuse as main transcript	c.135G>A	p.Pro45=	synonymous_variant	2/7	1	NM_021258.4	ENSP00000270800	P1

Frequencies

GnomAD3 genomes

AF:

0.371

AC:

56388

AN:

151844

Hom.:

11321

Cov.:

show subpopulations

Gnomad AFR

AF:

0.267

Gnomad AMI

AF:

0.426

Gnomad AMR

AF:

0.483

Gnomad ASJ

AF:

0.326

Gnomad EAS

AF:

0.745

Gnomad SAS

AF:

0.484

Gnomad FIN

AF:

0.358

Gnomad MID

AF:

0.225

Gnomad NFE

AF:

0.377

Gnomad OTH

AF:

0.380

GnomAD3 exomes

AF:

0.430

AC:

108117

AN:

251290

Hom.:

25188

AF XY:

0.423

AC XY:

57513

AN XY:

135826

show subpopulations

Gnomad AFR exome

AF:

0.264

Gnomad AMR exome

AF:

0.587

Gnomad ASJ exome

AF:

0.321

Gnomad EAS exome

AF:

0.736

Gnomad SAS exome

AF:

0.467

Gnomad FIN exome

AF:

0.357

Gnomad NFE exome

AF:

0.372

Gnomad OTH exome

AF:

0.397

GnomAD4 exome

AF:

0.402

AC:

587087

AN:

1461584

Hom.:

122438

Cov.:

AF XY:

0.402

AC XY:

292208

AN XY:

727100

show subpopulations

Gnomad4 AFR exome

AF:

0.254

Gnomad4 AMR exome

AF:

0.575

Gnomad4 ASJ exome

AF:

0.322

Gnomad4 EAS exome

AF:

0.738

Gnomad4 SAS exome

AF:

0.458

Gnomad4 FIN exome

AF:

0.357

Gnomad4 NFE exome

AF:

0.388

Gnomad4 OTH exome

AF:

0.399

GnomAD4 genome

AF:

0.371

AC:

56402

AN:

151962

Hom.:

11319

Cov.:

AF XY:

0.375

AC XY:

27850

AN XY:

74242

show subpopulations

Gnomad4 AFR

AF:

0.267

Gnomad4 AMR

AF:

0.484

Gnomad4 ASJ

AF:

0.326

Gnomad4 EAS

AF:

0.745

Gnomad4 SAS

AF:

0.483

Gnomad4 FIN

AF:

0.358

Gnomad4 NFE

AF:

0.377

Gnomad4 OTH

AF:

0.376

Alfa

AF:

0.371

Hom.:

17921

Bravo

AF:

0.377

Asia WGS

AF:

0.587

AC:

2041

AN:

3478

EpiCase

AF:

0.361

EpiControl

AF:

0.363

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

Jan 24, 2024

This variant is classified as Benign based on local population frequency. This variant was detected in 74% of patients studied by a panel of primary immunodeficiencies. Number of patients: 65. Only high quality variants are reported. -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.73

CADD

Benign

2.1

DANN

Benign

0.65

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