Variant 1-24120724-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_021258.4(IL22RA1):c.*81C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.644 in 1,310,466 control chromosomes in the GnomAD database, including 274,794 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.66 ( 33922 hom., cov: 35)

Exomes 𝑓: 0.64 ( 240872 hom. )

Consequence

IL22RA1
NM_021258.4 3_prime_UTR

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -1.75

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 -14 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.83).

BP6

Variant 1-24120724-G-A is Benign according to our data. Variant chr1-24120724-G-A is described in ClinVar as [Benign]. Clinvar id is 2688539.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.766 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.*81C>T		3_prime_UTR_variant	7/7	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.*81C>T		3_prime_UTR_variant	7/7	1	NM_021258.4	ENSP00000270800	P1

Frequencies

GnomAD3 genomes

AF:

0.662

AC:

100700

AN:

152076

Hom.:

33903

Cov.:

show subpopulations

Gnomad AFR

AF:

0.770

Gnomad AMI

AF:

0.718

Gnomad AMR

AF:

0.620

Gnomad ASJ

AF:

0.668

Gnomad EAS

AF:

0.716

Gnomad SAS

AF:

0.787

Gnomad FIN

AF:

0.467

Gnomad MID

AF:

0.668

Gnomad NFE

AF:

0.622

Gnomad OTH

AF:

0.655

GnomAD4 exome

AF:

0.642

AC:

743373

AN:

1158272

Hom.:

240872

Cov.:

AF XY:

0.646

AC XY:

371262

AN XY:

575148

show subpopulations

Gnomad4 AFR exome

AF:

0.780

Gnomad4 AMR exome

AF:

0.562

Gnomad4 ASJ exome

AF:

0.671

Gnomad4 EAS exome

AF:

0.720

Gnomad4 SAS exome

AF:

0.786

Gnomad4 FIN exome

AF:

0.482

Gnomad4 NFE exome

AF:

0.634

Gnomad4 OTH exome

AF:

0.658

GnomAD4 genome

AF:

0.662

AC:

100760

AN:

152194

Hom.:

33922

Cov.:

AF XY:

0.659

AC XY:

48996

AN XY:

74400

show subpopulations

Gnomad4 AFR

AF:

0.770

Gnomad4 AMR

AF:

0.620

Gnomad4 ASJ

AF:

0.668

Gnomad4 EAS

AF:

0.716

Gnomad4 SAS

AF:

0.787

Gnomad4 FIN

AF:

0.467

Gnomad4 NFE

AF:

0.622

Gnomad4 OTH

AF:

0.649

Alfa

AF:

0.632

Hom.:

40312

Bravo

AF:

0.670

Asia WGS

AF:

0.736

AC:

2560

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

Jan 24, 2024

This variant is classified as Benign based on local population frequency. This variant was detected in 85% of patients studied by a panel of primary immunodeficiencies. Number of patients: 75. Only high quality variants are reported. -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.83

CADD

Benign

0.026

DANN

Benign

0.37

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