rs3795302

Positions:

• chr1-24120626-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.*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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0300

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=-0.8).
• 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/exons	MANE	UniProt
IL22RA1	NM_021258.4	c.*179G>A		3_prime_UTR_variant	7/7	ENST00000270800.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
IL22RA1	ENST00000270800.2	c.*179G>A		3_prime_UTR_variant	7/7	1	NM_021258.4	P1

Frequencies

GnomAD3 genomes AF: 0.404 AC: 61381 AN: 152116 Hom.: 13105 Cov.: 34

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.: 5 AF XY: 0.439 AC XY: 103335 AN XY: 235156

Gnomad4 AFR exome AF: 0.310

Gnomad4 AMR exome AF: 0.557

Gnomad4 ASJ exome AF: 0.379

Gnomad4 EAS exome AF: 0.723

Gnomad4 SAS exome AF: 0.508

Gnomad4 FIN exome AF: 0.340

Gnomad4 NFE exome AF: 0.413

Gnomad4 OTH exome AF: 0.433

GnomAD4 genome AF: 0.403 AC: 61395 AN: 152234 Hom.: 13106 Cov.: 34 AF XY: 0.406 AC XY: 30188 AN XY: 74420

Gnomad4 AFR AF: 0.314

Gnomad4 AMR AF: 0.512

Gnomad4 ASJ AF: 0.384

Gnomad4 EAS AF: 0.713

Gnomad4 SAS AF: 0.533

Gnomad4 FIN AF: 0.339

Gnomad4 NFE AF: 0.411

Gnomad4 OTH AF: 0.413

Alfa AF: 0.416 Hom.: 13114

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
DANN	Benign	0.67

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: rs3795302; hg19: chr1-24447116; COSMIC: COSV54627523;