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GeneBe

1-24121594-G-A

Variant summary

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

The NM_021258.4(IL22RA1):c.936C>T(p.Pro312=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.293 in 1,612,038 control chromosomes in the GnomAD database, including 72,263 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.26 ( 5853 hom., cov: 32)
Exomes 𝑓: 0.30 ( 66410 hom. )

Consequence

IL22RA1
NM_021258.4 synonymous

Scores

2

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.116
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -15 ACMG points.

BP4
?
    BP4 - Multiple lines of computational evidence suggest no impact on gene or gene product (conservation, evolutionary, splicing impact, etc.)
Computational evidence support a benign effect (BayesDel_noAF=-0.79).
BP6
?
    BP6 - Reputable source recently reports variant as benign, but the evidence is not available to the laboratory to perform an independent evaluation
Variant 1-24121594-G-A is Benign according to our data. Variant chr1-24121594-G-A is described in ClinVar as [Benign]. Clinvar id is 2688433.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
    BP7 - A synonymous (silent) variant for which splicing prediction algorithms predict no impact to the splice consensus sequence nor the creation of a new splice site AND the nucleotide is not highly conserved
Synonymous conserved (PhyloP=0.116 with no splicing effect.
BA1
?
    BA1 - Allele frequency is >5% in Exome Sequencing Project, 1000 Genomes Project, or Exome Aggregation Consortium
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.313 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
IL22RA1NM_021258.4 linkuse as main transcriptc.936C>T p.Pro312= synonymous_variant 7/7 ENST00000270800.2

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
IL22RA1ENST00000270800.2 linkuse as main transcriptc.936C>T p.Pro312= synonymous_variant 7/71 NM_021258.4 P1

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.256
AC:
38886
AN:
151878
Hom.:
5844
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.112
Gnomad AMI
AF:
0.254
Gnomad AMR
AF:
0.225
Gnomad ASJ
AF:
0.301
Gnomad EAS
AF:
0.277
Gnomad SAS
AF:
0.198
Gnomad FIN
AF:
0.478
Gnomad MID
AF:
0.244
Gnomad NFE
AF:
0.316
Gnomad OTH
AF:
0.257
GnomAD3 exomes
AF:
0.289
AC:
72153
AN:
250016
Hom.:
11119
AF XY:
0.290
AC XY:
39189
AN XY:
135108
show subpopulations
Gnomad AFR exome
AF:
0.109
Gnomad AMR exome
AF:
0.231
Gnomad ASJ exome
AF:
0.298
Gnomad EAS exome
AF:
0.288
Gnomad SAS exome
AF:
0.201
Gnomad FIN exome
AF:
0.465
Gnomad NFE exome
AF:
0.321
Gnomad OTH exome
AF:
0.297
GnomAD4 exome
AF:
0.297
AC:
432911
AN:
1460040
Hom.:
66410
Cov.:
39
AF XY:
0.295
AC XY:
214154
AN XY:
726012
show subpopulations
Gnomad4 AFR exome
AF:
0.106
Gnomad4 AMR exome
AF:
0.228
Gnomad4 ASJ exome
AF:
0.299
Gnomad4 EAS exome
AF:
0.275
Gnomad4 SAS exome
AF:
0.198
Gnomad4 FIN exome
AF:
0.462
Gnomad4 NFE exome
AF:
0.306
Gnomad4 OTH exome
AF:
0.281
GnomAD4 genome
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.256
AC:
38904
AN:
151998
Hom.:
5853
Cov.:
32
AF XY:
0.261
AC XY:
19386
AN XY:
74308
show subpopulations
Gnomad4 AFR
AF:
0.112
Gnomad4 AMR
AF:
0.224
Gnomad4 ASJ
AF:
0.301
Gnomad4 EAS
AF:
0.277
Gnomad4 SAS
AF:
0.199
Gnomad4 FIN
AF:
0.478
Gnomad4 NFE
AF:
0.316
Gnomad4 OTH
AF:
0.263
Alfa
AF:
0.295
Hom.:
8977
Bravo
AF:
0.235
Asia WGS
AF:
0.242
AC:
839
AN:
3478
EpiCase
AF:
0.316
EpiControl
AF:
0.307

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 submitterclinical testingUnidad de Genómica Garrahan, Hospital de Pediatría GarrahanJan 24, 2024This variant is classified as Benign based on local population frequency. This variant was detected in 42% of patients studied by a panel of primary immunodeficiencies. Number of patients: 37. Only high quality variants are reported. -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.79
Cadd
Benign
2.1
Dann
Benign
0.50

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.

Other links and lift over

dbSNP: rs17852648; hg19: chr1-24448084; COSMIC: COSV54627858; API