rs2069778

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000226730.5(IL2):​c.208-1127C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.101 in 151,504 control chromosomes in the GnomAD database, including 1,040 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 0.10 ( 1040 hom., cov: 31)

Consequence

IL2
ENST00000226730.5 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0370
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]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.89).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.158 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
IL2NM_000586.4 linkuse as main transcriptc.208-1127C>T intron_variant ENST00000226730.5 NP_000577.2

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
IL2ENST00000226730.5 linkuse as main transcriptc.208-1127C>T intron_variant 1 NM_000586.4 ENSP00000226730 P1
IL2ENST00000477645.1 linkuse as main transcriptn.298-1127C>T intron_variant, non_coding_transcript_variant 3

Frequencies

GnomAD3 genomes
AF:
0.101
AC:
15315
AN:
151386
Hom.:
1040
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.0276
Gnomad AMI
AF:
0.184
Gnomad AMR
AF:
0.0747
Gnomad ASJ
AF:
0.0883
Gnomad EAS
AF:
0.000964
Gnomad SAS
AF:
0.0801
Gnomad FIN
AF:
0.108
Gnomad MID
AF:
0.0443
Gnomad NFE
AF:
0.160
Gnomad OTH
AF:
0.0910
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.101
AC:
15319
AN:
151504
Hom.:
1040
Cov.:
31
AF XY:
0.0973
AC XY:
7200
AN XY:
74026
show subpopulations
Gnomad4 AFR
AF:
0.0275
Gnomad4 AMR
AF:
0.0746
Gnomad4 ASJ
AF:
0.0883
Gnomad4 EAS
AF:
0.000966
Gnomad4 SAS
AF:
0.0806
Gnomad4 FIN
AF:
0.108
Gnomad4 NFE
AF:
0.160
Gnomad4 OTH
AF:
0.0895
Alfa
AF:
0.134
Hom.:
312
Bravo
AF:
0.0936
Asia WGS
AF:
0.0370
AC:
130
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
2.6
DANN
Benign
0.41

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.

Other links and lift over

dbSNP: rs2069778; hg19: chr4-123376135; API