Genetic Variant IL22RA2:c.-138C>T (chr6-137173485-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_052962.3(IL22RA2):c.-138C>T variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.503 in 152,134 control chromosomes in the GnomAD database, including 20,738 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 0.50 ( 20738 hom., cov: 33)

Exomes 𝑓: 0.50 ( 0 hom. )

Consequence

IL22RA2
NM_052962.3 5_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.162

Publications

10 publications found

Variant links:

Genes affected

IL22RA2 (HGNC:14901): (interleukin 22 receptor subunit alpha 2) This gene encodes a member of the class II cytokine receptor family. The encoded soluble protein specifically binds to and inhibits interleukin 22 activity by blocking the interaction of interleukin 22 with its cell surface receptor. The encoded protein may be important in the regulation of inflammatory response, and has been implicated in the regulation of tumorigenesis in the colon. Alternative splicing results in multiple transcript variants encoding distinct isoforms. [provided by RefSeq, Jul 2013]

IL22RA2 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=-0.96).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.699 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	MANE	Protein	UniProt
IL22RA2	NM_052962.3 link	c.-138C>T	5_prime_UTR_variant	Exon 1 of 7	ENST00000296980.7	NP_443194.1	Q969J5-1
IL22RA2	NM_181309.2 link	c.-138C>T	5_prime_UTR_variant	Exon 1 of 6		NP_851826.1	Q969J5-2
IL22RA2	NM_181310.2 link	c.-138C>T	5_prime_UTR_variant	Exon 1 of 5		NP_851827.1	Q969J5-3

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
IL22RA2	ENST00000296980.7 link	c.-138C>T	5_prime_UTR_variant	Exon 1 of 7	1	NM_052962.3	ENSP00000296980.2	Q969J5-1
IL22RA2	ENST00000349184.9 link	c.-138C>T	5_prime_UTR_variant	Exon 1 of 6	1		ENSP00000296979.4	Q969J5-2
IL22RA2	ENST00000339602.3 link	c.-138C>T	5_prime_UTR_variant	Exon 1 of 5	1		ENSP00000340920.3	Q969J5-3

Frequencies

GnomAD3 genomes

AF:

0.502

AC:

76367

AN:

152014

Hom.:

20686

Cov.:

show subpopulations

Gnomad AFR

AF:

0.705

Gnomad AMI

AF:

0.309

Gnomad AMR

AF:

0.497

Gnomad ASJ

AF:

0.539

Gnomad EAS

AF:

0.608

Gnomad SAS

AF:

0.535

Gnomad FIN

AF:

0.366

Gnomad MID

AF:

0.472

Gnomad NFE

AF:

0.391

Gnomad OTH

AF:

0.535

GnomAD4 exome

AF:

0.500

AC:

AN:

Hom.:

Cov.:

AF XY:

0.500

AC XY:

AN XY:

show subpopulations

African (AFR)

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AF:

0.500

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AC:

AN:

Other (OTH)

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.425

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.503

AC:

76473

AN:

152132

Hom.:

20738

Cov.:

AF XY:

0.504

AC XY:

37451

AN XY:

74374

show subpopulations

African (AFR)

AF:

0.706

AC:

29310

AN:

41522

American (AMR)

AF:

0.496

AC:

7588

AN:

15290

Ashkenazi Jewish (ASJ)

AF:

0.539

AC:

1869

AN:

3470

East Asian (EAS)

AF:

0.607

AC:

3148

AN:

5184

South Asian (SAS)

AF:

0.534

AC:

2575

AN:

4822

European-Finnish (FIN)

AF:

0.366

AC:

3867

AN:

10560

Middle Eastern (MID)

AF:

0.480

AC:

141

AN:

294

European-Non Finnish (NFE)

AF:

0.391

AC:

26558

AN:

67972

Other (OTH)

AF:

0.539

AC:

1136

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.506

Heterozygous variant carriers

1866

3733

5599

7466

9332

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

674

1348

2022

2696

3370

<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:

0.450

Hom.:

10172

Bravo

AF:

0.522

Asia WGS

AF:

0.612

AC:

2125

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.96

CADD

Benign

1.6

(source)

DANN

Benign

0.59

PhyloP100

-0.16

PromoterAI

-0.068

Neutral

(source)

Mutation Taster

=300/0

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

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over