chr1-24143324-T-C

Variant names:

• chr1-24143324-T-C
• rs4292900
• NM_021258.4:c.-242A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_021258.4(IL22RA1):​c.-242A>G variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.627 in 151,994 control chromosomes in the GnomAD database, including 31,682 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 0.63 (31682 hom., cov: 30)
• Consequence: IL22RA1 NM_021258.4 upstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.926
• Publications: 15 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=-0.74).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.963 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_021258.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	IL22RA1	NM_021258.4	MANE Select	c.-242A>G		upstream_gene	N/A	NP_067081.2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	IL22RA1	ENST00000270800.2	TSL:1 MANE Select	c.-242A>G		upstream_gene	N/A	ENSP00000270800.1	Q8N6P7
	IL22RA1	ENST00000873330.1		c.-242A>G		upstream_gene	N/A	ENSP00000543389.1
	IL22RA1	ENST00000873332.1		c.-242A>G		upstream_gene	N/A	ENSP00000543391.1

Frequencies

GnomAD3 genomes AF: 0.627 AC: 95272 AN: 151876 Hom.: 31678 Cov.: 30

Gnomad AFR AF: 0.410

Gnomad AMI AF: 0.781

Gnomad AMR AF: 0.704

Gnomad ASJ AF: 0.627

Gnomad EAS AF: 0.985

Gnomad SAS AF: 0.685

Gnomad FIN AF: 0.783

Gnomad MID AF: 0.509

Gnomad NFE AF: 0.685

Gnomad OTH AF: 0.638

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.627 AC: 95309 AN: 151994 Hom.: 31682 Cov.: 30 AF XY: 0.635 AC XY: 47131 AN XY: 74274

African (AFR) AF: 0.410 AC: 16970 AN: 41408

American (AMR) AF: 0.704 AC: 10744 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.627 AC: 2176 AN: 3472

East Asian (EAS) AF: 0.985 AC: 5099 AN: 5176

South Asian (SAS) AF: 0.684 AC: 3294 AN: 4814

European-Finnish (FIN) AF: 0.783 AC: 8287 AN: 10586

Middle Eastern (MID) AF: 0.507 AC: 149 AN: 294

European-Non Finnish (NFE) AF: 0.685 AC: 46527 AN: 67960

Other (OTH) AF: 0.641 AC: 1352 AN: 2110

Alfa AF: 0.661 Hom.: 55868

Bravo AF: 0.616

Asia WGS AF: 0.820 AC: 2849 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.74
CADD	Benign	0.68
DANN	Benign	0.74
PhyloP100		-0.93
PromoterAI		0.077	Neutral

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs4292900; hg19: chr1-24469814;