4-141678069-C-T
Variant names:
Variant summary
Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_000585.5(IL15):c.-100+21762C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.508 in 151,912 control chromosomes in the GnomAD database, including 19,913 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 0.51 ( 19913 hom., cov: 32)
Consequence
IL15
NM_000585.5 intron
NM_000585.5 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.819
Publications
7 publications found
Genes affected
IL15 (HGNC:5977): (interleukin 15) The protein encoded by this gene is a cytokine that regulates T and natural killer cell activation and proliferation. This cytokine and interleukine 2 share many biological activities. They are found to bind common hematopoietin receptor subunits, and may compete for the same receptor, and thus negatively regulate each other's activity. The number of CD8+ memory cells is shown to be controlled by a balance between this cytokine and IL2. This cytokine induces the activation of JAK kinases, as well as the phosphorylation and activation of transcription activators STAT3, STAT5, and STAT6. Studies of the mouse counterpart suggested that this cytokine may increase the expression of apoptosis inhibitor BCL2L1/BCL-x(L), possibly through the transcription activation activity of STAT6, and thus prevent apoptosis. Alternatively spliced transcript variants of this gene have been reported. [provided by RefSeq, Feb 2011]
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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=-0.84).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.826 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
IL15 | NM_000585.5 | c.-100+21762C>T | intron_variant | Intron 2 of 7 | ENST00000320650.9 | NP_000576.1 | ||
IL15 | NM_172175.3 | c.-501-10753C>T | intron_variant | Intron 2 of 9 | NP_751915.1 | |||
IL15 | NR_037840.3 | n.764+21762C>T | intron_variant | Intron 2 of 7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
IL15 | ENST00000320650.9 | c.-100+21762C>T | intron_variant | Intron 2 of 7 | 1 | NM_000585.5 | ENSP00000323505.4 | |||
IL15 | ENST00000296545.11 | c.-100+21762C>T | intron_variant | Intron 2 of 7 | 1 | ENSP00000296545.7 | ||||
IL15 | ENST00000529613.5 | c.-313-10753C>T | intron_variant | Intron 1 of 7 | 5 | ENSP00000435462.1 | ||||
IL15 | ENST00000514653.5 | c.-501-10753C>T | intron_variant | Intron 2 of 9 | 5 | ENSP00000422271.1 |
Frequencies
GnomAD3 genomes AF: 0.508 AC: 77122AN: 151794Hom.: 19906 Cov.: 32 show subpopulations
GnomAD3 genomes
AF:
AC:
77122
AN:
151794
Hom.:
Cov.:
32
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.508 AC: 77159AN: 151912Hom.: 19913 Cov.: 32 AF XY: 0.515 AC XY: 38256AN XY: 74242 show subpopulations
GnomAD4 genome
AF:
AC:
77159
AN:
151912
Hom.:
Cov.:
32
AF XY:
AC XY:
38256
AN XY:
74242
show subpopulations
African (AFR)
AF:
AC:
19962
AN:
41410
American (AMR)
AF:
AC:
7203
AN:
15262
Ashkenazi Jewish (ASJ)
AF:
AC:
1959
AN:
3470
East Asian (EAS)
AF:
AC:
4369
AN:
5158
South Asian (SAS)
AF:
AC:
3040
AN:
4818
European-Finnish (FIN)
AF:
AC:
6161
AN:
10538
Middle Eastern (MID)
AF:
AC:
122
AN:
294
European-Non Finnish (NFE)
AF:
AC:
32828
AN:
67938
Other (OTH)
AF:
AC:
1007
AN:
2114
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.503
Heterozygous variant carriers
0
1902
3805
5707
7610
9512
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
2427
AN:
3478
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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