rs16829209

Variant names:

• chr1-24134805-C-T
• rs16829209
• NM_021258.4:c.356-419G>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
IL22RA1	NM_021258.4	c.356-419G>A		intron_variant	Intron 3 of 6	ENST00000270800.2	NP_067081.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
IL22RA1	ENST00000270800.2	c.356-419G>A		intron_variant	Intron 3 of 6	1	NM_021258.4	ENSP00000270800.1

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

African (AFR) AF: 0.236 AC: 3647 AN: 15462

American (AMR) AF: 0.135 AC: 131 AN: 970

Ashkenazi Jewish (ASJ) AF: 0.218 AC: 1100 AN: 5052

East Asian (EAS) AF: 0.00195 AC: 7 AN: 3592

South Asian (SAS) AF: 0.215 AC: 3476 AN: 16130

European-Finnish (FIN) AF: 0.148 AC: 40 AN: 270

Middle Eastern (MID) AF: 0.258 AC: 411 AN: 1592

European-Non Finnish (NFE) AF: 0.161 AC: 120515 AN: 750122

Other (OTH) AF: 0.166 AC: 4458 AN: 26910

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

African (AFR) AF: 0.233 AC: 9677 AN: 41476

American (AMR) AF: 0.146 AC: 2234 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.231 AC: 803 AN: 3470

East Asian (EAS) AF: 0.00154 AC: 8 AN: 5188

South Asian (SAS) AF: 0.210 AC: 1012 AN: 4816

European-Finnish (FIN) AF: 0.133 AC: 1407 AN: 10592

Middle Eastern (MID) AF: 0.288 AC: 84 AN: 292

European-Non Finnish (NFE) AF: 0.166 AC: 11282 AN: 67996

Other (OTH) AF: 0.179 AC: 377 AN: 2110

Alfa AF: 0.176 Hom.: 1248

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
PhyloP100		-0.56
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs16829209; hg19: chr1-24461295;