Genetic Variant IL22:c.252+23A>G (chr12-68252741-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_020525.5(IL22):c.252+23A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.577 in 1,611,750 control chromosomes in the GnomAD database, including 271,208 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 0.58 ( 26049 hom., cov: 31)

Exomes 𝑓: 0.58 ( 245159 hom. )

Consequence

IL22
NM_020525.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.322

Publications

47 publications found

Variant links:

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]

IL22 links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.87).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.629 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_020525.5. 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
	IL22	NM_020525.5	MANE Select	c.252+23A>G		intron	N/A	NP_065386.1	Q9GZX6

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	IL22	ENST00000538666.6	TSL:1 MANE Select	c.252+23A>G		intron	N/A	ENSP00000442424.1	Q9GZX6
	IL22	ENST00000328087.6	TSL:1	c.252+23A>G		intron	N/A	ENSP00000329384.4	Q9GZX6

Frequencies

GnomAD3 genomes

AF:

0.582

AC:

88431

AN:

151854

Hom.:

26023

Cov.:

show subpopulations

Gnomad AFR

AF:

0.635

Gnomad AMI

AF:

0.561

Gnomad AMR

AF:

0.543

Gnomad ASJ

AF:

0.478

Gnomad EAS

AF:

0.482

Gnomad SAS

AF:

0.466

Gnomad FIN

AF:

0.534

Gnomad MID

AF:

0.430

Gnomad NFE

AF:

0.590

Gnomad OTH

AF:

0.538

GnomAD2 exomes

AF:

0.547

AC:

137220

AN:

250714

AF XY:

0.541

show subpopulations

Gnomad AFR exome

AF:

0.633

Gnomad AMR exome

AF:

0.526

Gnomad ASJ exome

AF:

0.471

Gnomad EAS exome

AF:

0.498

Gnomad FIN exome

AF:

0.550

Gnomad NFE exome

AF:

0.583

Gnomad OTH exome

AF:

0.539

GnomAD4 exome

AF:

0.576

AC:

841420

AN:

1459778

Hom.:

245159

Cov.:

AF XY:

0.571

AC XY:

414565

AN XY:

726348

show subpopulations

African (AFR)

AF:

0.630

AC:

21067

AN:

33426

American (AMR)

AF:

0.523

AC:

23401

AN:

44718

Ashkenazi Jewish (ASJ)

AF:

0.478

AC:

12493

AN:

26120

East Asian (EAS)

AF:

0.455

AC:

18070

AN:

39686

South Asian (SAS)

AF:

0.453

AC:

39026

AN:

86210

European-Finnish (FIN)

AF:

0.554

AC:

29560

AN:

53378

Middle Eastern (MID)

AF:

0.473

AC:

2720

AN:

5756

European-Non Finnish (NFE)

AF:

0.596

AC:

661379

AN:

1110170

Other (OTH)

AF:

0.559

AC:

33704

AN:

60314

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.484

Heterozygous variant carriers

17908

35817

53725

71634

89542

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

17964

35928

53892

71856

89820

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.582

AC:

88492

AN:

151972

Hom.:

26049

Cov.:

AF XY:

0.577

AC XY:

42855

AN XY:

74258

show subpopulations

African (AFR)

AF:

0.635

AC:

26304

AN:

41426

American (AMR)

AF:

0.543

AC:

8293

AN:

15276

Ashkenazi Jewish (ASJ)

AF:

0.478

AC:

1659

AN:

3472

East Asian (EAS)

AF:

0.482

AC:

2492

AN:

5166

South Asian (SAS)

AF:

0.467

AC:

2245

AN:

4808

European-Finnish (FIN)

AF:

0.534

AC:

5637

AN:

10550

Middle Eastern (MID)

AF:

0.435

AC:

128

AN:

294

European-Non Finnish (NFE)

AF:

0.590

AC:

40107

AN:

67970

Other (OTH)

AF:

0.532

AC:

1118

AN:

2102

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1842

3684

5526

7368

9210

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

738

1476

2214

2952

3690

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.573

Hom.:

33827

Bravo

AF:

0.583

Asia WGS

AF:

0.436

AC:

1519

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.87

CADD

Benign

1.3

(source)

DANN

Benign

0.26

PhyloP100

-0.32

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over