rs12722489

Variant names:

• chr10-6060049-C-T
• rs12722489
• NM_000417.3:c.64+2039G>A

GermlineCancer (beta)

Variant summary

Our verdict is Likely benign.

-4 Likely Benign

-7

-6

-1

0

+5

+6

+9

+10

BenignB

Likely BenignLB

UncertainVUS

Likely PathogenicLP

PathogenicP

The variant received -4 classification points (ACGS-UK Somatic Oncogenicity v2025). B1_Strong

The NM_000417.3(IL2RA):c.64+2039G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The gene IL2RA is a tumor suppressor gene (CancerMine: 1 TSG, 1 oncogene citations). The gene IL2RA is a known oncogene (CancerMine: 1 TSG, 1 oncogene citations). The variant allele was found at a cumulative frequency of 0.106 (AC=16,152) in the gnomAD database across 152,076 control chromosomes, including 1,103 homozygotes. The grpmax filtering allele frequency (95% CI) is 0.153. In-silico predictor (BayesDel (noAF)) classifies this variant as likely benign. Splicing prediction tools (SpliceAI) predict no significant impact on normal splicing. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.11 (1103 hom., cov: 31)
• Consequence: IL2RA NM_000417.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0320
• Publications: 113 publications found

Genes affected

IL2RA (HGNC:6008): (interleukin 2 receptor subunit alpha) The interleukin 2 (IL2) receptor alpha (IL2RA) and beta (IL2RB) chains, together with the common gamma chain (IL2RG), constitute the high-affinity IL2 receptor. Homodimeric alpha chains (IL2RA) result in low-affinity receptor, while homodimeric beta (IL2RB) chains produce a medium-affinity receptor. Normally an integral-membrane protein, soluble IL2RA has been isolated and determined to result from extracellular proteolyisis. Alternately-spliced IL2RA mRNAs have been isolated, but the significance of each is presently unknown. Mutations in this gene are associated with interleukin 2 receptor alpha deficiency. Patients with severe Coronavirus Disease 2019 (COVID-19), the disease caused by the novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), have significantly elevated levels of IL2R in their plasma. Similarly, serum IL-2R levels are found to be elevated in patients with different types of carcinomas. Certain IL2RA and IL2RB gene polymorphisms have been associated with lung cancer risk. [provided by RefSeq, Jul 2020]

IL2RA Gene-Disease associations (from GenCC):

• immunodeficiency due to CD25 deficiency

  Inheritance: AR Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: ClinGen, Labcorp Genetics (formerly Invitae), PanelApp Australia, Orphanet
• neonatal diabetes mellitus

  Inheritance: AR Classification: STRONG Submitted by: Genomics England PanelApp
• neonatal diabetes mellitus with congenital hypothyroidism

  Inheritance: AR Classification: STRONG Submitted by: Genomics England PanelApp
• type 1 diabetes mellitus 10

  Inheritance: AR Classification: STRONG Submitted by: Genomics England PanelApp

Classification according to ACGS-UK Somatic Oncogenicity v2025

Classification was made for transcript:

Our verdict: Likely_benign. The variant received -4 points.

Apply	Criterion Code & Title / Strength	Strength	Rationale / Clinical Context
	B1High frequency in general population		GnomAD effective popmax AF >1% — B1 stand-alone benign; GnomAD effective popmax AF = 0.153 — exceeds 1% threshold (B1 applied)

Variant Effect in Transcripts

Automated classification analysis was done for transcript: NM_000417.3. You can select a different transcript below to see updated classification assignments.

RefSeq Transcripts

Sel.	Gene / Transcript	Tags	HGVSc / HGVSp	Effect	Exon rank	Protein / UniProt
	IL2RA NM_000417.3	MANE Select	c.64+2039G>A	intron	Intron 1 of 7	Prot: NP_000408.1 UniProt:
	IL2RA NM_001308242.2		c.64+2039G>A	intron	Intron 1 of 6	Prot: NP_001295171.1 UniProt:
	IL2RA NM_001308243.2		c.64+2039G>A	intron	Intron 1 of 5	Prot: NP_001295172.1 UniProt:

IL2RA NM_000417.3

MANE Select

HGVSc / HGVSpc.64+2039G>A

Exon rankIntron 1 of 7

intron

Prot: NP_000408.1UniProt: P01589

IL2RA NM_001308242.2

HGVSc / HGVSpc.64+2039G>A

Exon rankIntron 1 of 6

intron

Prot: NP_001295171.1UniProt: Q5W005

IL2RA NM_001308243.2

HGVSc / HGVSpc.64+2039G>A

Exon rankIntron 1 of 5

intron

Prot: NP_001295172.1UniProt: H0Y5Z0

Ensembl Transcripts

Sel.	Gene / Transcript	Tags	HGVSc / HGVSp	Effect	Exon rank	Protein / UniProt
	IL2RA ENST00000379959.8	TSL:1MANE Select	c.64+2039G>A	intron	Intron 1 of 7	Prot: ENSP00000369293.3 UniProt:
	IL2RA ENST00000379954.5	TSL:1	c.64+2039G>A	intron	Intron 1 of 6	Prot: ENSP00000369287.1 UniProt:
	IL2RA ENST00000447847.2	TSL:1	c.64+2039G>A	intron	Intron 1 of 5	Prot: ENSP00000402024.2 UniProt:

IL2RA ENST00000379959.8

TSL:1MANE Select

HGVSc / HGVSpc.64+2039G>A

Exon rankIntron 1 of 7

intron

Prot: ENSP00000369293.3UniProt: P01589

IL2RA ENST00000379954.5

TSL:1

HGVSc / HGVSpc.64+2039G>A

Exon rankIntron 1 of 6

intron

Prot: ENSP00000369287.1UniProt: Q5W005

IL2RA ENST00000447847.2

TSL:1

HGVSc / HGVSpc.64+2039G>A

Exon rankIntron 1 of 5

intron

Prot: ENSP00000402024.2UniProt: H0Y5Z0

Frequencies

Allele frequencies (AF), counts (AC/AN), homozygotes and coverage

Common (AF > 0.05 / Hom > 5)

Rare (AF ≤ 0.0001 / Hom ≤ 1)

Source / population	AF	AC	Hom	AN	Coverage
Global population databases 4 sources Large-scale international reference populations
GnomAD3 genomes	AF: 0.106	AC:16165	Hom:1107	AN:151958	Cov:31
GnomAD4 genome	AF: 0.106	AC:16152	Hom:1103	AN:152076	Cov:31
TOPMed (Bravo)	AF: 0.0995	AC:	Hom:	AN:	Cov:
ALFA (dbGaP/dbSNP Allele Frequency Aggregator)	AF: 0.138	AC:90032	Hom:6719	AN:651304	Cov:
Local & regional cohorts 10 sources Population-specific and national genomic databases
ABraOM SABE-WGS-1171	AF: 0.0956	AC:224	Hom:13	AN:2342	Cov:
ChinaMAP Phase 1	AF: 0.129	AC:	Hom:	AN:	Cov:
Denmark Genome	AF: 0.173	AC:52	Hom:	AN:300	Cov:
GenomeAsia100K	AF: 0.141	AC:490	Hom:	AN:3478	Cov:
Korea4K (4,157 Koreans)	AF: 0.109	AC:785	Hom:	AN:7234	Cov:
Qatari Genome	AF: 0.0398	AC:7	Hom:	AN:176	Cov:
ToMMo 61KJPN (+60KJPN MNV)	AF: 0.103	AC:12620	Hom:679	AN:122696	Cov:
Turkish Variome	AF: 0.0724	AC:112	Hom:7	AN:1546	Cov:
UK10K	AF: 0.163	AC:1234	Hom:	AN:7562	Cov:
WBBC (Westlake BioBank for Chinese) pilot	AF: 0.137	AC:1224	Hom:100	AN:8960	Cov:

Showing 14 sources

ClinVar

Not reported in ClinVar

Computational Scores

Algorithm	Calibrated pred.	Score	Prediction
AlphaGenome AVI	Benign	0.65
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.5
DANN	Benign	0.53
GPN-Star LLR	N/A	0.35
GPN-Star score	N/A	-0.35
Mutation Taster	N/A	100/0	polymorphism (auto)
PhyloP100	Benign	0.032

Showing 8 of 8 scores

Splicing Scores

Algorithm	Calibrated pred.	Score	Prediction
Pangolin (max)	Benign	0.0
SpliceAI score (max)	Benign	0.0	Details are displayed if max score is > 0.2

Showing 2 of 2 scores

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

MaveDB functional evidence

MaveDB is a public repository of laboratory assays that test the effect of thousands of variants at once — treat this as supporting research data and interpret it with great caution; it is not a clinical classification.

No MaveDB functional evidence found for this variant.

Other links and lift over

dbSNP: rs12722489;

hg19: chr10-6102012;

ACMG debug oncogenicity

ACGS debug oncogenicity

ACMG debug germline

Submit to ClinVar