rs2069778

Variant names:

• chr4-122454980-G-A
• rs2069778
• NM_000586.4:c.208-1127C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_000586.4(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 NM_000586.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0370
• Publications: 33 publications found

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]

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
IL2	NM_000586.4	c.208-1127C>T		intron_variant	Intron 2 of 3	ENST00000226730.5	NP_000577.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
IL2	ENST00000226730.5	c.208-1127C>T		intron_variant	Intron 2 of 3	1	NM_000586.4	ENSP00000226730.5
IL2	ENST00000477645.1	n.298-1127C>T		intron_variant	Intron 1 of 2	3

Frequencies

GnomAD3 genomes AF: 0.101 AC: 15315 AN: 151386 Hom.: 1040 Cov.: 31

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

African (AFR) AF: 0.0275 AC: 1137 AN: 41380

American (AMR) AF: 0.0746 AC: 1133 AN: 15178

Ashkenazi Jewish (ASJ) AF: 0.0883 AC: 305 AN: 3454

East Asian (EAS) AF: 0.000966 AC: 5 AN: 5176

South Asian (SAS) AF: 0.0806 AC: 388 AN: 4816

European-Finnish (FIN) AF: 0.108 AC: 1134 AN: 10542

Middle Eastern (MID) AF: 0.0510 AC: 15 AN: 294

European-Non Finnish (NFE) AF: 0.160 AC: 10847 AN: 67654

Other (OTH) AF: 0.0895 AC: 188 AN: 2100

Alfa AF: 0.131 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
PhyloP100		0.037
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs2069778; hg19: chr4-123376135;