Variant rs3136618 details in Genebe, Genetics Data Aggregator

Variant summary

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

The NM_002189.4(IL15RA):c.616+21G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.501 in 1,608,780 control chromosomes in the GnomAD database, including 204,477 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 0.53 ( 22175 hom., cov: 32)

Exomes 𝑓: 0.50 ( 182302 hom. )

Consequence

IL15RA
NM_002189.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.46

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:

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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=-0.84).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.647 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
IL15RA	NM_002189.4 linkuse as main transcript	c.616+21G>A		intron_variant		ENST00000379977.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
IL15RA	ENST00000379977.8 linkuse as main transcript	c.616+21G>A		intron_variant		1	NM_002189.4	A2	Q13261-1

Frequencies

GnomAD3 genomes

AF:

0.531

AC:

80731

AN:

151904

Hom.:

22143

Cov.:

show subpopulations

Gnomad AFR

AF:

0.654

Gnomad AMI

AF:

0.523

Gnomad AMR

AF:

0.510

Gnomad ASJ

AF:

0.535

Gnomad EAS

AF:

0.424

Gnomad SAS

AF:

0.551

Gnomad FIN

AF:

0.433

Gnomad MID

AF:

0.481

Gnomad NFE

AF:

0.485

Gnomad OTH

AF:

0.511

GnomAD3 exomes

AF:

0.503

AC:

125429

AN:

249390

Hom.:

32106

AF XY:

0.501

AC XY:

67573

AN XY:

134886

show subpopulations

Gnomad AFR exome

AF:

0.665

Gnomad AMR exome

AF:

0.525

Gnomad ASJ exome

AF:

0.522

Gnomad EAS exome

AF:

0.414

Gnomad SAS exome

AF:

0.562

Gnomad FIN exome

AF:

0.444

Gnomad NFE exome

AF:

0.481

Gnomad OTH exome

AF:

0.491

GnomAD4 exome

AF:

0.498

AC:

725073

AN:

1456756

Hom.:

182302

Cov.:

AF XY:

0.499

AC XY:

361360

AN XY:

724844

show subpopulations

Gnomad4 AFR exome

AF:

0.662

Gnomad4 AMR exome

AF:

0.524

Gnomad4 ASJ exome

AF:

0.530

Gnomad4 EAS exome

AF:

0.427

Gnomad4 SAS exome

AF:

0.564

Gnomad4 FIN exome

AF:

0.454

Gnomad4 NFE exome

AF:

0.490

Gnomad4 OTH exome

AF:

0.504

GnomAD4 genome

AF:

0.532

AC:

80822

AN:

152024

Hom.:

22175

Cov.:

AF XY:

0.529

AC XY:

39285

AN XY:

74294

show subpopulations

Gnomad4 AFR

AF:

0.654

Gnomad4 AMR

AF:

0.510

Gnomad4 ASJ

AF:

0.535

Gnomad4 EAS

AF:

0.424

Gnomad4 SAS

AF:

0.550

Gnomad4 FIN

AF:

0.433

Gnomad4 NFE

AF:

0.485

Gnomad4 OTH

AF:

0.510

Alfa

AF:

0.488

Hom.:

40958

Bravo

AF:

0.541

Asia WGS

AF:

0.496

AC:

1727

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.84

CADD

Benign

0.68

DANN

Benign

0.64

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.

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