chr1-24141971-G-A

Variant names:

• chr1-24141971-G-A
• rs4648936
• NM_021258.4:c.43+1069C>T

Variant summary

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

The NM_021258.4(IL22RA1):​c.43+1069C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.61 in 152,036 control chromosomes in the GnomAD database, including 30,679 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 0.61 (30679 hom., cov: 32)
• Consequence: IL22RA1 NM_021258.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.604
• Publications: 8 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=-0.88).
• 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.43+1069C>T		intron	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.43+1069C>T		intron	N/A	ENSP00000270800.1	Q8N6P7
	IL22RA1	ENST00000873330.1		c.43+1069C>T		intron	N/A	ENSP00000543389.1
	IL22RA1	ENST00000873332.1		c.43+1069C>T		intron	N/A	ENSP00000543391.1

Frequencies

GnomAD3 genomes AF: 0.611 AC: 92755 AN: 151920 Hom.: 30673 Cov.: 32

Gnomad AFR AF: 0.352

Gnomad AMI AF: 0.779

Gnomad AMR AF: 0.698

Gnomad ASJ AF: 0.626

Gnomad EAS AF: 0.985

Gnomad SAS AF: 0.682

Gnomad FIN AF: 0.782

Gnomad MID AF: 0.509

Gnomad NFE AF: 0.685

Gnomad OTH AF: 0.628

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

GnomAD4 genome AF: 0.610 AC: 92793 AN: 152036 Hom.: 30679 Cov.: 32 AF XY: 0.618 AC XY: 45916 AN XY: 74308

African (AFR) AF: 0.352 AC: 14571 AN: 41440

American (AMR) AF: 0.699 AC: 10680 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.626 AC: 2172 AN: 3468

East Asian (EAS) AF: 0.985 AC: 5091 AN: 5168

South Asian (SAS) AF: 0.681 AC: 3285 AN: 4822

European-Finnish (FIN) AF: 0.782 AC: 8261 AN: 10558

Middle Eastern (MID) AF: 0.510 AC: 149 AN: 292

European-Non Finnish (NFE) AF: 0.685 AC: 46543 AN: 67978

Other (OTH) AF: 0.631 AC: 1332 AN: 2112

Alfa AF: 0.623 Hom.: 3986

Bravo AF: 0.597

Asia WGS AF: 0.817 AC: 2838 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.59
DANN	Benign	0.44
PhyloP100		-0.60
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: rs4648936; hg19: chr1-24468461;