22-37148446-G-A

Position:

• chr22-37148446-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_000878.5(IL2RB):​c.-34+1379C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.207 in 152,080 control chromosomes in the GnomAD database, including 3,528 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 0.21 (3528 hom., cov: 32)
• Consequence: IL2RB NM_000878.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -4.32

Genes affected

IL2RB (HGNC:6009): (interleukin 2 receptor subunit beta) The interleukin 2 receptor, which is involved in T cell-mediated immune responses, is present in 3 forms with respect to ability to bind interleukin 2. The low affinity form is a monomer of the alpha subunit and is not involved in signal transduction. The intermediate affinity form consists of an alpha/beta subunit heterodimer, while the high affinity form consists of an alpha/beta/gamma subunit heterotrimer. Both the intermediate and high affinity forms of the receptor are involved in receptor-mediated endocytosis and transduction of mitogenic signals from interleukin 2. The protein encoded by this gene represents the beta subunit and is a type I membrane protein. The use of alternative promoters results in multiple transcript variants encoding the same protein. The protein is primarily expressed in the hematopoietic system. The use by some variants of an alternate promoter in an upstream long terminal repeat (LTR) results in placenta-specific expression. [provided by RefSeq, Sep 2016]

IL2RB (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.255 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
IL2RB	NM_000878.5	c.-34+1379C>T		intron_variant		ENST00000216223.10	NP_000869.1
IL2RB	NM_001346222.1	c.-33-4241C>T		intron_variant			NP_001333151.1
IL2RB	NM_001346223.2	c.-33-4241C>T		intron_variant			NP_001333152.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
IL2RB	ENST00000216223.10	c.-34+1379C>T		intron_variant		1	NM_000878.5	ENSP00000216223.5

Frequencies

GnomAD3 genomes AF: 0.207 AC: 31481 AN: 151962 Hom.: 3533 Cov.: 32

Gnomad AFR AF: 0.127

Gnomad AMI AF: 0.274

Gnomad AMR AF: 0.173

Gnomad ASJ AF: 0.259

Gnomad EAS AF: 0.102

Gnomad SAS AF: 0.142

Gnomad FIN AF: 0.298

Gnomad MID AF: 0.229

Gnomad NFE AF: 0.258

Gnomad OTH AF: 0.209

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.207 AC: 31485 AN: 152080 Hom.: 3528 Cov.: 32 AF XY: 0.206 AC XY: 15333 AN XY: 74340

Gnomad4 AFR AF: 0.127

Gnomad4 AMR AF: 0.173

Gnomad4 ASJ AF: 0.259

Gnomad4 EAS AF: 0.102

Gnomad4 SAS AF: 0.142

Gnomad4 FIN AF: 0.298

Gnomad4 NFE AF: 0.258

Gnomad4 OTH AF: 0.205

Alfa AF: 0.226 Hom.: 922

Bravo AF: 0.197

Asia WGS AF: 0.130 AC: 457 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.047
DANN	Benign	0.81

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: rs3218255; hg19: chr22-37544486;