rs2069840
Variant names:
Variant summary
Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_000600.5(IL6):c.324+147C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.286 in 631,248 control chromosomes in the GnomAD database, including 28,463 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 0.27 ( 6315 hom., cov: 33)
Exomes 𝑓: 0.29 ( 22148 hom. )
Consequence
IL6
NM_000600.5 intron
NM_000600.5 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.509
Genes affected
IL6 (HGNC:6018): (interleukin 6) This gene encodes a cytokine that functions in inflammation and the maturation of B cells. In addition, the encoded protein has been shown to be an endogenous pyrogen capable of inducing fever in people with autoimmune diseases or infections. The protein is primarily produced at sites of acute and chronic inflammation, where it is secreted into the serum and induces a transcriptional inflammatory response through interleukin 6 receptor, alpha. The functioning of this gene is implicated in a wide variety of inflammation-associated disease states, including suspectibility to diabetes mellitus and systemic juvenile rheumatoid arthritis. Elevated levels of the encoded protein have been found in virus infections, including COVID-19 (disease caused by SARS-CoV-2). [provided by RefSeq, Aug 2020]
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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=-0.64).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.348 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
IL6 | NM_000600.5 | c.324+147C>G | intron_variant | Intron 3 of 4 | ENST00000258743.10 | NP_000591.1 | ||
IL6 | NM_001371096.1 | c.255+147C>G | intron_variant | Intron 3 of 4 | NP_001358025.1 | |||
IL6 | NM_001318095.2 | c.96+147C>G | intron_variant | Intron 2 of 3 | NP_001305024.1 | |||
IL6 | XM_005249745.6 | c.486+147C>G | intron_variant | Intron 2 of 2 | XP_005249802.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.273 AC: 41529AN: 152042Hom.: 6317 Cov.: 33 show subpopulations
GnomAD3 genomes
AF:
AC:
41529
AN:
152042
Hom.:
Cov.:
33
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:
GnomAD4 exome AF: 0.290 AC: 138704AN: 479088Hom.: 22148 AF XY: 0.286 AC XY: 72511AN XY: 253444 show subpopulations
GnomAD4 exome
AF:
AC:
138704
AN:
479088
Hom.:
AF XY:
AC XY:
72511
AN XY:
253444
Gnomad4 AFR exome
AF:
AC:
2196
AN:
13152
Gnomad4 AMR exome
AF:
AC:
7792
AN:
22940
Gnomad4 ASJ exome
AF:
AC:
3689
AN:
14772
Gnomad4 EAS exome
AF:
AC:
2116
AN:
31364
Gnomad4 SAS exome
AF:
AC:
9230
AN:
48208
Gnomad4 FIN exome
AF:
AC:
9435
AN:
39188
Gnomad4 NFE exome
AF:
AC:
95561
AN:
278730
Gnomad4 Remaining exome
AF:
AC:
7892
AN:
27078
Heterozygous variant carriers
0
4575
9151
13726
18302
22877
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Exome Het
Exome Hom
Variant carriers
0
456
912
1368
1824
2280
<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: 0.273 AC: 41526AN: 152160Hom.: 6315 Cov.: 33 AF XY: 0.268 AC XY: 19915AN XY: 74406 show subpopulations
GnomAD4 genome
AF:
AC:
41526
AN:
152160
Hom.:
Cov.:
33
AF XY:
AC XY:
19915
AN XY:
74406
Gnomad4 AFR
AF:
AC:
0.165695
AN:
0.165695
Gnomad4 AMR
AF:
AC:
0.34402
AN:
0.34402
Gnomad4 ASJ
AF:
AC:
0.261521
AN:
0.261521
Gnomad4 EAS
AF:
AC:
0.0648148
AN:
0.0648148
Gnomad4 SAS
AF:
AC:
0.173651
AN:
0.173651
Gnomad4 FIN
AF:
AC:
0.233711
AN:
0.233711
Gnomad4 NFE
AF:
AC:
0.35204
AN:
0.35204
Gnomad4 OTH
AF:
AC:
0.2772
AN:
0.2772
Heterozygous variant carriers
0
1522
3044
4565
6087
7609
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Genome Het
Genome Hom
Variant carriers
0
416
832
1248
1664
2080
<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:
431
AN:
3478
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
Mutation Taster
=100/0
polymorphism (auto)
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