Variant rs2296139 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1

The NM_002189.4(IL15RA):c.219G>A(p.Thr73Thr) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.14 in 1,613,654 control chromosomes in the GnomAD database, including 17,420 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 0.16 ( 2087 hom., cov: 32)

Exomes 𝑓: 0.14 ( 15333 hom. )

Consequence

IL15RA
NM_002189.4 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -4.03

Variant links:

Genes affected

IL15RA (HGNC:5978): (interleukin 15 receptor subunit alpha) This gene encodes a cytokine receptor that specifically binds interleukin 15 (IL15) with high affinity. The receptors of IL15 and IL2 share two subunits, IL2R beta and IL2R gamma. This forms the basis of many overlapping biological activities of IL15 and IL2. The protein encoded by this gene is structurally related to IL2R alpha, an additional IL2-specific alpha subunit necessary for high affinity IL2 binding. Unlike IL2RA, IL15RA is capable of binding IL15 with high affinity independent of other subunits, which suggests distinct roles between IL15 and IL2. This receptor is reported to enhance cell proliferation and expression of apoptosis inhibitor BCL2L1/BCL2-XL and BCL2. Multiple alternatively spliced transcript variants of this gene have been reported.[provided by RefSeq, Apr 2010]

IL15RA links:

IL15RA (HGNC:):

IL15RA links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -13 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.8).

BP7

Synonymous conserved (PhyloP=-4.03 with no splicing effect.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.291 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
IL15RA	NM_002189.4 linkuse as main transcript	c.219G>A	p.Thr73Thr	synonymous_variant	2/7	ENST00000379977.8	NP_002180.1	Q13261-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
IL15RA	ENST00000379977.8 linkuse as main transcript	c.219G>A	p.Thr73Thr	synonymous_variant	2/7	1	NM_002189.4	ENSP00000369312.3		Q13261-1

Frequencies

GnomAD3 genomes

AF:

0.158

AC:

23996

AN:

151984

Hom.:

2074

Cov.:

show subpopulations

Gnomad AFR

AF:

0.170

Gnomad AMI

AF:

0.0932

Gnomad AMR

AF:

0.218

Gnomad ASJ

AF:

0.159

Gnomad EAS

AF:

0.303

Gnomad SAS

AF:

0.141

Gnomad FIN

AF:

0.116

Gnomad MID

AF:

0.142

Gnomad NFE

AF:

0.134

Gnomad OTH

AF:

0.169

GnomAD3 exomes

AF:

0.166

AC:

41777

AN:

251178

Hom.:

4158

AF XY:

0.161

AC XY:

21900

AN XY:

135744

show subpopulations

Gnomad AFR exome

AF:

0.168

Gnomad AMR exome

AF:

0.268

Gnomad ASJ exome

AF:

0.154

Gnomad EAS exome

AF:

0.310

Gnomad SAS exome

AF:

0.138

Gnomad FIN exome

AF:

0.117

Gnomad NFE exome

AF:

0.130

Gnomad OTH exome

AF:

0.155

GnomAD4 exome

AF:

0.138

AC:

201874

AN:

1461552

Hom.:

15333

Cov.:

AF XY:

0.138

AC XY:

100455

AN XY:

727042

show subpopulations

Gnomad4 AFR exome

AF:

0.172

Gnomad4 AMR exome

AF:

0.258

Gnomad4 ASJ exome

AF:

0.155

Gnomad4 EAS exome

AF:

0.299

Gnomad4 SAS exome

AF:

0.143

Gnomad4 FIN exome

AF:

0.112

Gnomad4 NFE exome

AF:

0.127

Gnomad4 OTH exome

AF:

0.142

GnomAD4 genome

AF:

0.158

AC:

24044

AN:

152102

Hom.:

2087

Cov.:

AF XY:

0.160

AC XY:

11869

AN XY:

74358

show subpopulations

Gnomad4 AFR

AF:

0.170

Gnomad4 AMR

AF:

0.219

Gnomad4 ASJ

AF:

0.159

Gnomad4 EAS

AF:

0.303

Gnomad4 SAS

AF:

0.140

Gnomad4 FIN

AF:

0.116

Gnomad4 NFE

AF:

0.134

Gnomad4 OTH

AF:

0.167

Alfa

AF:

0.142

Hom.:

2928

Bravo

AF:

0.170

Asia WGS

AF:

0.170

AC:

594

AN:

3478

EpiCase

AF:

0.142

EpiControl

AF:

0.141

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.80

CADD

Benign

0.036

DANN

Benign

0.66

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.020

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over