Variant rs3136614 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.382+32C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.801 in 1,405,840 control chromosomes in the GnomAD database, including 452,508 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 0.83 ( 52869 hom., cov: 32)

Exomes 𝑓: 0.80 ( 399639 hom. )

Consequence

IL15RA
NM_002189.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.509

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:

LOC107984200 (HGNC:):

LOC107984200 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=-0.9).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.943 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.382+32C>T		intron_variant		ENST00000379977.8
LOC107984200	XR_001747348.2 linkuse as main transcript	n.1321-473G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
IL15RA	ENST00000379977.8 linkuse as main transcript	c.382+32C>T		intron_variant		1	NM_002189.4	A2	Q13261-1

Frequencies

GnomAD3 genomes

AF:

0.831

AC:

126414

AN:

152052

Hom.:

52812

Cov.:

show subpopulations

Gnomad AFR

AF:

0.880

Gnomad AMI

AF:

0.563

Gnomad AMR

AF:

0.839

Gnomad ASJ

AF:

0.816

Gnomad EAS

AF:

0.965

Gnomad SAS

AF:

0.895

Gnomad FIN

AF:

0.888

Gnomad MID

AF:

0.764

Gnomad NFE

AF:

0.782

Gnomad OTH

AF:

0.807

GnomAD3 exomes

AF:

0.830

AC:

127055

AN:

152992

Hom.:

53009

AF XY:

0.827

AC XY:

70353

AN XY:

85036

show subpopulations

Gnomad AFR exome

AF:

0.883

Gnomad AMR exome

AF:

0.895

Gnomad ASJ exome

AF:

0.804

Gnomad EAS exome

AF:

0.969

Gnomad SAS exome

AF:

0.898

Gnomad FIN exome

AF:

0.885

Gnomad NFE exome

AF:

0.776

Gnomad OTH exome

AF:

0.810

GnomAD4 exome

AF:

0.797

AC:

999206

AN:

1253670

Hom.:

399639

Cov.:

AF XY:

0.799

AC XY:

496987

AN XY:

622172

show subpopulations

Gnomad4 AFR exome

AF:

0.879

Gnomad4 AMR exome

AF:

0.876

Gnomad4 ASJ exome

AF:

0.806

Gnomad4 EAS exome

AF:

0.968

Gnomad4 SAS exome

AF:

0.897

Gnomad4 FIN exome

AF:

0.881

Gnomad4 NFE exome

AF:

0.776

Gnomad4 OTH exome

AF:

0.813

GnomAD4 genome

AF:

0.832

AC:

126531

AN:

152170

Hom.:

52869

Cov.:

AF XY:

0.838

AC XY:

62367

AN XY:

74388

show subpopulations

Gnomad4 AFR

AF:

0.880

Gnomad4 AMR

AF:

0.840

Gnomad4 ASJ

AF:

0.816

Gnomad4 EAS

AF:

0.965

Gnomad4 SAS

AF:

0.896

Gnomad4 FIN

AF:

0.888

Gnomad4 NFE

AF:

0.782

Gnomad4 OTH

AF:

0.809

Alfa

AF:

0.786

Hom.:

65402

Bravo

AF:

0.828

Asia WGS

AF:

0.932

AC:

3243

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

0.64

DANN

Benign

0.43

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