rs11265618
Variant names:
Variant summary
Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_000565.4(IL6R):c.1160+3035C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.211 in 152,112 control chromosomes in the GnomAD database, including 3,856 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 0.21 ( 3856 hom., cov: 32)
Consequence
IL6R
NM_000565.4 intron
NM_000565.4 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.813
Publications
49 publications found
Genes affected
IL6R (HGNC:6019): (interleukin 6 receptor) This gene encodes a subunit of the interleukin 6 (IL6) receptor complex. Interleukin 6 is a potent pleiotropic cytokine that regulates cell growth and differentiation and plays an important role in the immune response. The IL6 receptor is a protein complex consisting of this protein and interleukin 6 signal transducer (IL6ST/GP130/IL6-beta), a receptor subunit also shared by many other cytokines. Dysregulated production of IL6 and this receptor are implicated in the pathogenesis of many diseases, such as multiple myeloma, autoimmune diseases and prostate cancer. Alternatively spliced transcript variants encoding distinct isoforms have been identified in this gene. A pseudogene of this gene is found on chromosome 9. [provided by RefSeq, Aug 2020]
IL6R Gene-Disease associations (from GenCC):
- hyper-IgE recurrent infection syndrome 5, autosomal recessiveInheritance: AR Classification: STRONG, MODERATE, LIMITED Submitted by: Ambry Genetics, Labcorp Genetics (formerly Invitae), ClinGen
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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=-0.96).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.325 is higher than 0.05.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
IL6R | ENST00000368485.8 | c.1160+3035C>T | intron_variant | Intron 9 of 9 | 1 | NM_000565.4 | ENSP00000357470.3 | |||
IL6R | ENST00000344086.8 | c.1067-7518C>T | intron_variant | Intron 8 of 8 | 1 | ENSP00000340589.4 | ||||
IL6R | ENST00000502679.1 | n.473+3035C>T | intron_variant | Intron 1 of 1 | 2 | |||||
IL6R | ENST00000507256.1 | n.358+3035C>T | intron_variant | Intron 4 of 4 | 4 |
Frequencies
GnomAD3 genomes AF: 0.211 AC: 32078AN: 151994Hom.: 3839 Cov.: 32 show subpopulations
GnomAD3 genomes
AF:
AC:
32078
AN:
151994
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: 0.211 AC: 32131AN: 152112Hom.: 3856 Cov.: 32 AF XY: 0.209 AC XY: 15533AN XY: 74358 show subpopulations
GnomAD4 genome
AF:
AC:
32131
AN:
152112
Hom.:
Cov.:
32
AF XY:
AC XY:
15533
AN XY:
74358
show subpopulations
African (AFR)
AF:
AC:
13666
AN:
41464
American (AMR)
AF:
AC:
2132
AN:
15280
Ashkenazi Jewish (ASJ)
AF:
AC:
667
AN:
3472
East Asian (EAS)
AF:
AC:
544
AN:
5180
South Asian (SAS)
AF:
AC:
865
AN:
4824
European-Finnish (FIN)
AF:
AC:
1767
AN:
10584
Middle Eastern (MID)
AF:
AC:
53
AN:
294
European-Non Finnish (NFE)
AF:
AC:
11832
AN:
67990
Other (OTH)
AF:
AC:
425
AN:
2112
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.503
Heterozygous variant carriers
0
1253
2506
3760
5013
6266
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Genome Het
Genome Hom
Variant carriers
0
336
672
1008
1344
1680
<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:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
632
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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