rs4393147

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_000565.4(IL6R):​c.949+5451C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.326 in 151,926 control chromosomes in the GnomAD database, including 9,381 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 0.33 ( 9381 hom., cov: 32)

Consequence

IL6R
NM_000565.4 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.242
Variant links:
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]

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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=-0.95).
BA1
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.486 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
IL6RNM_000565.4 linkc.949+5451C>T intron_variant ENST00000368485.8 NP_000556.1 P08887-1A0N0L5

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
IL6RENST00000368485.8 linkc.949+5451C>T intron_variant 1 NM_000565.4 ENSP00000357470.3 P08887-1

Frequencies

GnomAD3 genomes
AF:
0.327
AC:
49586
AN:
151808
Hom.:
9380
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.138
Gnomad AMI
AF:
0.522
Gnomad AMR
AF:
0.496
Gnomad ASJ
AF:
0.386
Gnomad EAS
AF:
0.372
Gnomad SAS
AF:
0.294
Gnomad FIN
AF:
0.287
Gnomad MID
AF:
0.363
Gnomad NFE
AF:
0.402
Gnomad OTH
AF:
0.351
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.326
AC:
49590
AN:
151926
Hom.:
9381
Cov.:
32
AF XY:
0.322
AC XY:
23888
AN XY:
74246
show subpopulations
Gnomad4 AFR
AF:
0.138
Gnomad4 AMR
AF:
0.496
Gnomad4 ASJ
AF:
0.386
Gnomad4 EAS
AF:
0.372
Gnomad4 SAS
AF:
0.294
Gnomad4 FIN
AF:
0.287
Gnomad4 NFE
AF:
0.402
Gnomad4 OTH
AF:
0.347
Alfa
AF:
0.319
Hom.:
1313
Bravo
AF:
0.341
Asia WGS
AF:
0.294
AC:
1025
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.95
CADD
Benign
5.4
DANN
Benign
0.65

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.

Other links and lift over

dbSNP: rs4393147; hg19: chr1-154414037; API