10-6010992-G-C

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BS1 BS2

The NM_000417.3(IL2RA):c.*1880C>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0455 in 152,300 control chromosomes in the GnomAD database, including 183 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.045 (182 hom., cov: 32)
  • Exomes 𝑓: 0.066 (1 hom.)
• Consequence: IL2RA NM_000417.3 3_prime_UTR
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.106

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]

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BP6: Variant 10-6010992-G-C is Benign according to our data. Variant chr10-6010992-G-C is described in ClinVar as [Benign]. Clinvar id is 300215.Status of the report is criteria_provided_single_submitter, 1 stars.
• BS1: Variant frequency is greater than expected in population sas. gnomad4 allele frequency = 0.0455 (6923/152164) while in subpopulation SAS AF= 0.0481 (232/4826). AF 95% confidence interval is 0.0466. There are 182 homozygotes in gnomad4. There are 3550 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd at 182 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
IL2RA	NM_000417.3	c.*1880C>G		3_prime_UTR_variant	8/8	ENST00000379959.8
IL2RA	NM_001308242.2	c.*1880C>G		3_prime_UTR_variant	7/7
IL2RA	NM_001308243.2	c.*1880C>G		3_prime_UTR_variant	6/6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
IL2RA	ENST00000379959.8	c.*1880C>G		3_prime_UTR_variant	8/8	1	NM_000417.3	P1
IL2RA	ENST00000649218.1	n.2514C>G		non_coding_transcript_exon_variant	4/4

Frequencies

GnomAD3 genomes AF: 0.0455 AC: 6922 AN: 152046 Hom.: 182 Cov.: 32

Gnomad AFR AF: 0.0310

Gnomad AMI AF: 0.0307

Gnomad AMR AF: 0.0475

Gnomad ASJ AF: 0.0703

Gnomad EAS AF: 0.0115

Gnomad SAS AF: 0.0487

Gnomad FIN AF: 0.0904

Gnomad MID AF: 0.0633

Gnomad NFE AF: 0.0480

Gnomad OTH AF: 0.0522

GnomAD4 exome AF: 0.0662 AC: 9 AN: 136 Hom.: 1 Cov.: 0 AF XY: 0.0658 AC XY: 5 AN XY: 76

Gnomad4 EAS exome AF: 0.0682

Gnomad4 NFE exome AF: 0.00

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.0455 AC: 6923 AN: 152164 Hom.: 182 Cov.: 32 AF XY: 0.0477 AC XY: 3550 AN XY: 74376

Gnomad4 AFR AF: 0.0310

Gnomad4 AMR AF: 0.0474

Gnomad4 ASJ AF: 0.0703

Gnomad4 EAS AF: 0.0118

Gnomad4 SAS AF: 0.0481

Gnomad4 FIN AF: 0.0904

Gnomad4 NFE AF: 0.0480

Gnomad4 OTH AF: 0.0512

Alfa AF: 0.0246 Hom.: 14

Bravo AF: 0.0406

Asia WGS AF: 0.0320 AC: 110 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

Immunodeficiency due to CD25 deficiency Benign:1

Benign, criteria provided, single submitter

clinical testing

Illumina Laboratory Services, Illumina

Jan 13, 2018

This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
Cadd	Benign	0.070
Dann	Benign	0.42

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

Other links and lift over

dbSNP: rs12722607; hg19: chr10-6052955;