dbSNP rs3093387: IL21R:c.*464G>A (chr16-27449747-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_181078.3(IL21R):c.*464G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.166 in 241,522 control chromosomes in the GnomAD database, including 4,191 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 0.16 ( 2354 hom., cov: 33)

Exomes 𝑓: 0.18 ( 1837 hom. )

Consequence

IL21R
NM_181078.3 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.357

Publications

8 publications found

Variant links:

Genes affected

IL21R (HGNC:6006): (interleukin 21 receptor) The protein encoded by this gene is a cytokine receptor for interleukin 21 (IL21). It belongs to the type I cytokine receptors, and has been shown to form a heterodimeric receptor complex with the common gamma-chain, a receptor subunit also shared by the receptors for interleukin 2, 4, 7, 9, and 15. This receptor transduces the growth promoting signal of IL21, and is important for the proliferation and differentiation of T cells, B cells, and natural killer (NK) cells. The ligand binding of this receptor leads to the activation of multiple downstream signaling molecules, including JAK1, JAK3, STAT1, and STAT3. Knockout studies of a similar gene in mouse suggest a role for this gene in regulating immunoglobulin production. Three alternatively spliced transcript variants have been described. [provided by RefSeq, Jul 2010]

IL21R links:

IL21R-AS1 (HGNC:27551): (IL21R antisense RNA 1)

IL21R-AS1 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=-0.84).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.222 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
IL21R	NM_181078.3 link	c.*464G>A		3_prime_UTR_variant	Exon 9 of 9	ENST00000337929.8	NP_851564.1	Q9HBE5

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
IL21R	ENST00000337929.8 link	c.*464G>A	3_prime_UTR_variant	Exon 9 of 9	1	NM_181078.3	ENSP00000338010.3	Q9HBE5
IL21R	ENST00000395754.4 link	c.*464G>A	3_prime_UTR_variant	Exon 9 of 9	1		ENSP00000379103.4	Q9HBE5
IL21R-AS1	ENST00000563191.1 link	n.537C>T	non_coding_transcript_exon_variant	Exon 3 of 3	2
IL21R	ENST00000564089.5 link	c.*464G>A	3_prime_UTR_variant	Exon 10 of 10	5		ENSP00000456707.1	Q9HBE5

Frequencies

GnomAD3 genomes

AF:

0.156

AC:

23712

AN:

152126

Hom.:

2354

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0426

Gnomad AMI

AF:

0.220

Gnomad AMR

AF:

0.196

Gnomad ASJ

AF:

0.233

Gnomad EAS

AF:

0.00404

Gnomad SAS

AF:

0.0735

Gnomad FIN

AF:

0.168

Gnomad MID

AF:

0.252

Gnomad NFE

AF:

0.225

Gnomad OTH

AF:

0.180

GnomAD4 exome

AF:

0.183

AC:

16296

AN:

89278

Hom.:

1837

Cov.:

AF XY:

0.183

AC XY:

7590

AN XY:

41566

show subpopulations

African (AFR)

AF:

0.0483

AC:

198

AN:

4100

American (AMR)

AF:

0.174

AC:

717

AN:

4120

Ashkenazi Jewish (ASJ)

AF:

0.243

AC:

1276

AN:

5254

East Asian (EAS)

AF:

0.000775

AC:

AN:

11616

South Asian (SAS)

AF:

0.0552

AC:

AN:

1396

European-Finnish (FIN)

AF:

0.136

AC:

AN:

280

Middle Eastern (MID)

AF:

0.236

AC:

119

AN:

504

European-Non Finnish (NFE)

AF:

0.227

AC:

12457

AN:

54880

Other (OTH)

AF:

0.197

AC:

1405

AN:

7128

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.491

Heterozygous variant carriers

656

1312

1968

2624

3280

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.156

AC:

23713

AN:

152244

Hom.:

2354

Cov.:

AF XY:

0.154

AC XY:

11451

AN XY:

74440

show subpopulations

African (AFR)

AF:

0.0428

AC:

1777

AN:

41562

American (AMR)

AF:

0.197

AC:

3006

AN:

15296

Ashkenazi Jewish (ASJ)

AF:

0.233

AC:

808

AN:

3466

East Asian (EAS)

AF:

0.00404

AC:

AN:

5192

South Asian (SAS)

AF:

0.0728

AC:

351

AN:

4824

European-Finnish (FIN)

AF:

0.168

AC:

1784

AN:

10604

Middle Eastern (MID)

AF:

0.247

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.225

AC:

15319

AN:

67990

Other (OTH)

AF:

0.178

AC:

376

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.489

Heterozygous variant carriers

965

1930

2894

3859

4824

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.208

Hom.:

2948

Bravo

AF:

0.154

Asia WGS

AF:

0.0330

AC:

114

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.84

CADD

Benign

4.2

(source)

DANN

Benign

0.55

PhyloP100

0.36

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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rs3093387

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over