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GeneBe

rs2104286

Variant summary

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

The NM_000417.3(IL2RA):c.64+5006A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.18 in 152,254 control chromosomes in the GnomAD database, including 2,975 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 0.18 ( 2975 hom., cov: 32)

Consequence

IL2RA
NM_000417.3 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.790
Variant links:
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]

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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=-0.92).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.257 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
IL2RANM_000417.3 linkuse as main transcriptc.64+5006A>G intron_variant ENST00000379959.8
IL2RANM_001308242.2 linkuse as main transcriptc.64+5006A>G intron_variant
IL2RANM_001308243.2 linkuse as main transcriptc.64+5006A>G intron_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
IL2RAENST00000379959.8 linkuse as main transcriptc.64+5006A>G intron_variant 1 NM_000417.3 P1

Frequencies

GnomAD3 genomes
AF:
0.180
AC:
27363
AN:
152136
Hom.:
2978
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0634
Gnomad AMI
AF:
0.283
Gnomad AMR
AF:
0.129
Gnomad ASJ
AF:
0.247
Gnomad EAS
AF:
0.132
Gnomad SAS
AF:
0.185
Gnomad FIN
AF:
0.188
Gnomad MID
AF:
0.158
Gnomad NFE
AF:
0.260
Gnomad OTH
AF:
0.166
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.180
AC:
27352
AN:
152254
Hom.:
2975
Cov.:
32
AF XY:
0.175
AC XY:
13004
AN XY:
74452
show subpopulations
Gnomad4 AFR
AF:
0.0633
Gnomad4 AMR
AF:
0.129
Gnomad4 ASJ
AF:
0.247
Gnomad4 EAS
AF:
0.131
Gnomad4 SAS
AF:
0.184
Gnomad4 FIN
AF:
0.188
Gnomad4 NFE
AF:
0.260
Gnomad4 OTH
AF:
0.164
Alfa
AF:
0.240
Hom.:
9090
Bravo
AF:
0.171
Asia WGS
AF:
0.158
AC:
550
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.92
Cadd
Benign
0.52
Dann
Benign
0.55

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: rs2104286; hg19: chr10-6099045; COSMIC: COSV56921491; API