rs1179251

chr12-68251271-C-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_020525.5(IL22):c.462+242G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.182 in 152,014 control chromosomes in the GnomAD database, including 3,856 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 (3856 hom., cov: 32)
• Consequence: IL22 NM_020525.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.12

Genes affected

IL22 (HGNC:14900): (interleukin 22) This gene is a member of the IL10 family of cytokines that mediate cellular inflammatory responses. The encoded protein functions in antimicrobial defense at mucosal surfaces and in tissue repair. This protein also has pro-inflammatory properties and plays a role in in the pathogenesis of several intestinal diseases. The encoded protein is a crucial cytokine that regulates host immunity in infectious diseases, including COVID-19 (disease caused by SARS-CoV-2). [provided by RefSeq, Dec 2021]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.362 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
IL22	NM_020525.5	c.462+242G>C		intron_variant		ENST00000538666.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
IL22	ENST00000538666.6	c.462+242G>C		intron_variant		1	NM_020525.5	P1
IL22	ENST00000328087.6	c.462+242G>C		intron_variant		1		P1

Frequencies

GnomAD3 genomes AF: 0.181 AC: 27560 AN: 151896 Hom.: 3838 Cov.: 32

Gnomad AFR AF: 0.367

Gnomad AMI AF: 0.0504

Gnomad AMR AF: 0.148

Gnomad ASJ AF: 0.143

Gnomad EAS AF: 0.327

Gnomad SAS AF: 0.305

Gnomad FIN AF: 0.0569

Gnomad MID AF: 0.158

Gnomad NFE AF: 0.0801

Gnomad OTH AF: 0.172

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

GnomAD4 genome AF: 0.182 AC: 27637 AN: 152014 Hom.: 3856 Cov.: 32 AF XY: 0.183 AC XY: 13570 AN XY: 74302

Gnomad4 AFR AF: 0.367

Gnomad4 AMR AF: 0.149

Gnomad4 ASJ AF: 0.143

Gnomad4 EAS AF: 0.327

Gnomad4 SAS AF: 0.305

Gnomad4 FIN AF: 0.0569

Gnomad4 NFE AF: 0.0801

Gnomad4 OTH AF: 0.178

Alfa AF: 0.129 Hom.: 298

Bravo AF: 0.195

Asia WGS AF: 0.318 AC: 1100 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	0.021
Dann	Benign	0.19

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: rs1179251; hg19: chr12-68645051;