Variant rs2069763 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP6BA1

The ENST00000226730.5(IL2):c.114G>T(p.Leu38=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.331 in 1,606,330 control chromosomes in the GnomAD database, including 93,631 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in Lovd as Benign (no stars).

Frequency

Genomes: 𝑓 0.29 ( 7518 hom., cov: 32)

Exomes 𝑓: 0.34 ( 86113 hom. )

Consequence

IL2
ENST00000226730.5 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0760

Variant links:

Genes affected

IL2 (HGNC:6001): (interleukin 2) This gene is a member of the interleukin 2 (IL2) cytokine subfamily which includes IL4, IL7, IL9, IL15, IL21, erythropoietin, and thrombopoietin. The protein encoded by this gene is a secreted cytokine produced by activated CD4+ and CD8+ T lymphocytes, that is important for the proliferation of T and B lymphocytes. The receptor of this cytokine (IL2R) is a heterotrimeric protein complex whose gamma chain is also shared by IL4 and IL7. The expression of this gene in mature thymocytes is monoallelic, which represents an unusual regulatory mode for controlling the precise expression of a single gene. The targeted disruption of a similar gene in mice leads to ulcerative colitis-like disease, which suggests an essential role of this gene in the immune response to antigenic stimuli. [provided by RefSeq, Sep 2020]

IL2 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -13 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.57).

BP6

Variant 4-122456327-C-A is Benign according to our data. Variant chr4-122456327-C-A is described in Lovd as [Benign].

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.461 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
IL2	NM_000586.4 linkuse as main transcript	c.114G>T	p.Leu38=	synonymous_variant	1/4	ENST00000226730.5	NP_000577.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
IL2	ENST00000226730.5 linkuse as main transcript	c.114G>T	p.Leu38=	synonymous_variant	1/4	1	NM_000586.4	ENSP00000226730	P1
IL2	ENST00000477645.1 linkuse as main transcript	n.114G>T		non_coding_transcript_exon_variant	1/3	3

Frequencies

GnomAD3 genomes

AF:

0.290

AC:

43941

AN:

151608

Hom.:

7517

Cov.:

show subpopulations

Gnomad AFR

AF:

0.116

Gnomad AMI

AF:

0.197

Gnomad AMR

AF:

0.395

Gnomad ASJ

AF:

0.210

Gnomad EAS

AF:

0.476

Gnomad SAS

AF:

0.264

Gnomad FIN

AF:

0.472

Gnomad MID

AF:

0.174

Gnomad NFE

AF:

0.338

Gnomad OTH

AF:

0.271

GnomAD3 exomes

AF:

0.356

AC:

88751

AN:

249066

Hom.:

17277

AF XY:

0.347

AC XY:

46732

AN XY:

134654

show subpopulations

Gnomad AFR exome

AF:

0.112

Gnomad AMR exome

AF:

0.501

Gnomad ASJ exome

AF:

0.218

Gnomad EAS exome

AF:

0.473

Gnomad SAS exome

AF:

0.271

Gnomad FIN exome

AF:

0.475

Gnomad NFE exome

AF:

0.343

Gnomad OTH exome

AF:

0.333

GnomAD4 exome

AF:

0.335

AC:

487565

AN:

1454604

Hom.:

86113

Cov.:

AF XY:

0.332

AC XY:

240311

AN XY:

723892

show subpopulations

Gnomad4 AFR exome

AF:

0.0987

Gnomad4 AMR exome

AF:

0.487

Gnomad4 ASJ exome

AF:

0.220

Gnomad4 EAS exome

AF:

0.492

Gnomad4 SAS exome

AF:

0.270

Gnomad4 FIN exome

AF:

0.470

Gnomad4 NFE exome

AF:

0.335

Gnomad4 OTH exome

AF:

0.299

GnomAD4 genome

AF:

0.290

AC:

43943

AN:

151726

Hom.:

7518

Cov.:

AF XY:

0.297

AC XY:

21980

AN XY:

74130

show subpopulations

Gnomad4 AFR

AF:

0.116

Gnomad4 AMR

AF:

0.395

Gnomad4 ASJ

AF:

0.210

Gnomad4 EAS

AF:

0.477

Gnomad4 SAS

AF:

0.262

Gnomad4 FIN

AF:

0.472

Gnomad4 NFE

AF:

0.338

Gnomad4 OTH

AF:

0.271

Alfa

AF:

0.315

Hom.:

9024

Bravo

AF:

0.279

Asia WGS

AF:

0.300

AC:

1042

AN:

3478

EpiCase

AF:

0.309

EpiControl

AF:

0.311

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.57

CADD

Benign

5.5

DANN

Benign

0.59

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over