dbSNP rs3795302: IL22RA1:c.*179G>A (chr1-24120626-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_021258.4(IL22RA1):c.*179G>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 0.429 in 608,064 control chromosomes in the GnomAD database, including 59,303 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.40 ( 13106 hom., cov: 34)

Exomes 𝑓: 0.44 ( 46197 hom. )

Consequence

IL22RA1
NM_021258.4 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0300

Publications

7 publications found

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 was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.8).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.694 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
IL22RA1	NM_021258.4 link	c.*179G>A		3_prime_UTR_variant	Exon 7 of 7	ENST00000270800.2	NP_067081.2	Q8N6P7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
IL22RA1	ENST00000270800.2 link	c.*179G>A		3_prime_UTR_variant	Exon 7 of 7	1	NM_021258.4	ENSP00000270800.1		Q8N6P7

Frequencies

GnomAD3 genomes

AF:

0.404

AC:

61381

AN:

152116

Hom.:

13105

Cov.:

show subpopulations

Gnomad AFR

AF:

0.314

Gnomad AMI

AF:

0.467

Gnomad AMR

AF:

0.511

Gnomad ASJ

AF:

0.384

Gnomad EAS

AF:

0.713

Gnomad SAS

AF:

0.534

Gnomad FIN

AF:

0.339

Gnomad MID

AF:

0.329

Gnomad NFE

AF:

0.411

Gnomad OTH

AF:

0.418

GnomAD4 exome

AF:

0.437

AC:

199332

AN:

455830

Hom.:

46197

Cov.:

AF XY:

0.439

AC XY:

103335

AN XY:

235156

show subpopulations

African (AFR)

AF:

0.310

AC:

3970

AN:

12788

American (AMR)

AF:

0.557

AC:

9583

AN:

17190

Ashkenazi Jewish (ASJ)

AF:

0.379

AC:

5058

AN:

13336

East Asian (EAS)

AF:

0.723

AC:

22055

AN:

30488

South Asian (SAS)

AF:

0.508

AC:

17796

AN:

35046

European-Finnish (FIN)

AF:

0.340

AC:

12696

AN:

37372

Middle Eastern (MID)

AF:

0.337

AC:

709

AN:

2102

European-Non Finnish (NFE)

AF:

0.413

AC:

116287

AN:

281688

Other (OTH)

AF:

0.433

AC:

11178

AN:

25820

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

5173

10346

15519

20692

25865

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

1124

2248

3372

4496

5620

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.403

AC:

61395

AN:

152234

Hom.:

13106

Cov.:

AF XY:

0.406

AC XY:

30188

AN XY:

74420

show subpopulations

African (AFR)

AF:

0.314

AC:

13031

AN:

41550

American (AMR)

AF:

0.512

AC:

7837

AN:

15308

Ashkenazi Jewish (ASJ)

AF:

0.384

AC:

1332

AN:

3468

East Asian (EAS)

AF:

0.713

AC:

3692

AN:

5178

South Asian (SAS)

AF:

0.533

AC:

2574

AN:

4832

European-Finnish (FIN)

AF:

0.339

AC:

3593

AN:

10592

Middle Eastern (MID)

AF:

0.330

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.411

AC:

27941

AN:

67990

Other (OTH)

AF:

0.413

AC:

874

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1949

3897

5846

7794

9743

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

590

1180

1770

2360

2950

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.416

Hom.:

15334

Bravo

AF:

0.412

Asia WGS

AF:

0.585

AC:

2033

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.80

CADD

Benign

7.4

(source)

DANN

Benign

0.67

PhyloP100

-0.030

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over