dbSNP rs2296135: IL15RA:n.1349T>G (chr10-5952731-A-C) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000534292.5(IL15RA):n.1349T>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.551 in 265,304 control chromosomes in the GnomAD database, including 42,050 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 0.57 ( 26213 hom., cov: 33)

Exomes 𝑓: 0.52 ( 15837 hom. )

Consequence

IL15RA
ENST00000534292.5 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.326

Publications

40 publications found

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 was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.97).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.747 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
IL15RA	NM_002189.4 link	c.*364T>G		3_prime_UTR_variant	Exon 7 of 7	ENST00000379977.8	NP_002180.1	Q13261-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
IL15RA	ENST00000379977.8 link	c.*364T>G		3_prime_UTR_variant	Exon 7 of 7	1	NM_002189.4	ENSP00000369312.3		Q13261-1

Frequencies

GnomAD3 genomes

AF:

0.574

AC:

87247

AN:

151992

Hom.:

26174

Cov.:

show subpopulations

Gnomad AFR

AF:

0.753

Gnomad AMI

AF:

0.659

Gnomad AMR

AF:

0.489

Gnomad ASJ

AF:

0.539

Gnomad EAS

AF:

0.435

Gnomad SAS

AF:

0.563

Gnomad FIN

AF:

0.430

Gnomad MID

AF:

0.570

Gnomad NFE

AF:

0.519

Gnomad OTH

AF:

0.556

GnomAD4 exome

AF:

0.520

AC:

58812

AN:

113194

Hom.:

15837

Cov.:

AF XY:

0.522

AC XY:

30358

AN XY:

58180

show subpopulations

African (AFR)

AF:

0.752

AC:

2512

AN:

3340

American (AMR)

AF:

0.463

AC:

2327

AN:

5024

Ashkenazi Jewish (ASJ)

AF:

0.551

AC:

1833

AN:

3324

East Asian (EAS)

AF:

0.431

AC:

3002

AN:

6964

South Asian (SAS)

AF:

0.579

AC:

5668

AN:

9788

European-Finnish (FIN)

AF:

0.485

AC:

3042

AN:

6272

Middle Eastern (MID)

AF:

0.565

AC:

297

AN:

526

European-Non Finnish (NFE)

AF:

0.514

AC:

36621

AN:

71264

Other (OTH)

AF:

0.525

AC:

3510

AN:

6692

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.512

Heterozygous variant carriers

1351

2703

4054

5406

6757

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

294

588

882

1176

1470

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.574

AC:

87341

AN:

152110

Hom.:

26213

Cov.:

AF XY:

0.568

AC XY:

42185

AN XY:

74334

show subpopulations

African (AFR)

AF:

0.754

AC:

31284

AN:

41512

American (AMR)

AF:

0.489

AC:

7468

AN:

15272

Ashkenazi Jewish (ASJ)

AF:

0.539

AC:

1873

AN:

3472

East Asian (EAS)

AF:

0.435

AC:

2254

AN:

5176

South Asian (SAS)

AF:

0.562

AC:

2712

AN:

4828

European-Finnish (FIN)

AF:

0.430

AC:

4541

AN:

10564

Middle Eastern (MID)

AF:

0.568

AC:

167

AN:

294

European-Non Finnish (NFE)

AF:

0.519

AC:

35268

AN:

67968

Other (OTH)

AF:

0.555

AC:

1173

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

1859

3717

5576

7434

9293

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

724

1448

2172

2896

3620

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.531

Hom.:

49178

Bravo

AF:

0.584

Asia WGS

AF:

0.515

AC:

1791

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.97

CADD

Benign

2.1

(source)

DANN

Benign

0.48

PhyloP100

-0.33

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.0

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over