chr1-154447416-G-A
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.950-709G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. 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 0.28 ( 5191 hom., cov: 15)
Consequence
IL6R
NM_000565.4 intron
NM_000565.4 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.281
Publications
25 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=-1.0).
BA1
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.432 is higher than 0.05.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.278 AC: 28707AN: 103118Hom.: 5192 Cov.: 15 show subpopulations
GnomAD3 genomes
AF:
AC:
28707
AN:
103118
Hom.:
Cov.:
15
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: 0.278 AC: 28697AN: 103160Hom.: 5191 Cov.: 15 AF XY: 0.271 AC XY: 12963AN XY: 47922 show subpopulations
GnomAD4 genome
AF:
AC:
28697
AN:
103160
Hom.:
Cov.:
15
AF XY:
AC XY:
12963
AN XY:
47922
show subpopulations
African (AFR)
AF:
AC:
2683
AN:
27562
American (AMR)
AF:
AC:
3687
AN:
8296
Ashkenazi Jewish (ASJ)
AF:
AC:
942
AN:
2626
East Asian (EAS)
AF:
AC:
966
AN:
3326
South Asian (SAS)
AF:
AC:
689
AN:
3082
European-Finnish (FIN)
AF:
AC:
939
AN:
4400
Middle Eastern (MID)
AF:
AC:
70
AN:
166
European-Non Finnish (NFE)
AF:
AC:
18029
AN:
51652
Other (OTH)
AF:
AC:
420
AN:
1388
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.448
Heterozygous variant carriers
0
631
1262
1892
2523
3154
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Genome Het
Genome Hom
Variant carriers
0
258
516
774
1032
1290
<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.:
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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