rs16829209

chr1-24134805-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_021258.4(IL22RA1):c.356-419G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.165 in 972,238 control chromosomes in the GnomAD database, including 13,823 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 0.18 (2637 hom., cov: 32)
  • Exomes 𝑓: 0.16 (11186 hom.)
• Consequence: IL22RA1 NM_021258.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.565

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.229 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
IL22RA1	NM_021258.4	c.356-419G>A		intron_variant		ENST00000270800.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
IL22RA1	ENST00000270800.2	c.356-419G>A		intron_variant		1	NM_021258.4	P1

Frequencies

GnomAD3 genomes AF: 0.177 AC: 26960 AN: 152020 Hom.: 2636 Cov.: 32

Gnomad AFR AF: 0.233

Gnomad AMI AF: 0.111

Gnomad AMR AF: 0.146

Gnomad ASJ AF: 0.231

Gnomad EAS AF: 0.00154

Gnomad SAS AF: 0.210

Gnomad FIN AF: 0.133

Gnomad MID AF: 0.283

Gnomad NFE AF: 0.166

Gnomad OTH AF: 0.180

GnomAD4 exome AF: 0.163 AC: 133785 AN: 820100 Hom.: 11186 AF XY: 0.164 AC XY: 62122 AN XY: 379020

Gnomad4 AFR exome AF: 0.236

Gnomad4 AMR exome AF: 0.135

Gnomad4 ASJ exome AF: 0.218

Gnomad4 EAS exome AF: 0.00195

Gnomad4 SAS exome AF: 0.215

Gnomad4 FIN exome AF: 0.148

Gnomad4 NFE exome AF: 0.161

Gnomad4 OTH exome AF: 0.166

GnomAD4 genome AF: 0.177 AC: 26985 AN: 152138 Hom.: 2637 Cov.: 32 AF XY: 0.175 AC XY: 13018 AN XY: 74410

Gnomad4 AFR AF: 0.233

Gnomad4 AMR AF: 0.146

Gnomad4 ASJ AF: 0.231

Gnomad4 EAS AF: 0.00154

Gnomad4 SAS AF: 0.210

Gnomad4 FIN AF: 0.133

Gnomad4 NFE AF: 0.166

Gnomad4 OTH AF: 0.179

Alfa AF: 0.176 Hom.: 1129

Bravo AF: 0.177

Asia WGS AF: 0.0860 AC: 301 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
Cadd	Benign	1.1
Dann	Benign	0.59

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

Other links and lift over

dbSNP: rs16829209; hg19: chr1-24461295;