1-24139769-T-C

Variant names:

• chr1-24139769-T-C
• rs10751768
• NM_021258.4:c.44-1055A>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.44-1055A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.37 in 152,100 control chromosomes in the GnomAD database, including 11,295 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 0.37 (11295 hom., cov: 32)
• Consequence: IL22RA1 NM_021258.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0760
• Publications: 5 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=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.728 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
IL22RA1	NM_021258.4	c.44-1055A>G		intron_variant	Intron 1 of 6	ENST00000270800.2	NP_067081.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
IL22RA1	ENST00000270800.2	c.44-1055A>G		intron_variant	Intron 1 of 6	1	NM_021258.4	ENSP00000270800.1

Frequencies

GnomAD3 genomes AF: 0.370 AC: 56257 AN: 151982 Hom.: 11297 Cov.: 32

Gnomad AFR AF: 0.262

Gnomad AMI AF: 0.424

Gnomad AMR AF: 0.483

Gnomad ASJ AF: 0.325

Gnomad EAS AF: 0.748

Gnomad SAS AF: 0.485

Gnomad FIN AF: 0.358

Gnomad MID AF: 0.225

Gnomad NFE AF: 0.378

Gnomad OTH AF: 0.382

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

GnomAD4 genome AF: 0.370 AC: 56265 AN: 152100 Hom.: 11295 Cov.: 32 AF XY: 0.374 AC XY: 27834 AN XY: 74358

African (AFR) AF: 0.262 AC: 10851 AN: 41480

American (AMR) AF: 0.483 AC: 7382 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.325 AC: 1127 AN: 3472

East Asian (EAS) AF: 0.747 AC: 3875 AN: 5184

South Asian (SAS) AF: 0.485 AC: 2334 AN: 4816

European-Finnish (FIN) AF: 0.358 AC: 3791 AN: 10592

Middle Eastern (MID) AF: 0.221 AC: 65 AN: 294

European-Non Finnish (NFE) AF: 0.377 AC: 25657 AN: 67968

Other (OTH) AF: 0.378 AC: 796 AN: 2108

Alfa AF: 0.383 Hom.: 8909

Bravo AF: 0.375

Asia WGS AF: 0.589 AC: 2046 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	2.1
DANN	Benign	0.41
PhyloP100		0.076
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: rs10751768; hg19: chr1-24466259; COSMIC: COSV54627989;