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GeneBe

rs2069840

Variant summary

Our verdict is Benign. Variant got -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

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.509
Variant links:
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 made for transcript

Verdict is Benign. Variant got -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/exons MANE UniProt
IL6NM_000600.5 linkuse as main transcriptc.324+147C>G intron_variant ENST00000258743.10
IL6NM_001318095.2 linkuse as main transcriptc.96+147C>G intron_variant
IL6NM_001371096.1 linkuse as main transcriptc.255+147C>G intron_variant
IL6XM_005249745.6 linkuse as main transcriptc.486+147C>G intron_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
IL6ENST00000258743.10 linkuse as main transcriptc.324+147C>G intron_variant 1 NM_000600.5 P1

Frequencies

GnomAD3 genomes
AF:
0.273
AC:
41529
AN:
152042
Hom.:
6317
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.166
Gnomad AMI
AF:
0.282
Gnomad AMR
AF:
0.344
Gnomad ASJ
AF:
0.262
Gnomad EAS
AF:
0.0647
Gnomad SAS
AF:
0.173
Gnomad FIN
AF:
0.234
Gnomad MID
AF:
0.206
Gnomad NFE
AF:
0.352
Gnomad OTH
AF:
0.281
GnomAD4 exome
AF:
0.290
AC:
138704
AN:
479088
Hom.:
22148
AF XY:
0.286
AC XY:
72511
AN XY:
253444
show subpopulations
Gnomad4 AFR exome
AF:
0.167
Gnomad4 AMR exome
AF:
0.340
Gnomad4 ASJ exome
AF:
0.250
Gnomad4 EAS exome
AF:
0.0675
Gnomad4 SAS exome
AF:
0.191
Gnomad4 FIN exome
AF:
0.241
Gnomad4 NFE exome
AF:
0.343
Gnomad4 OTH exome
AF:
0.291
GnomAD4 genome
AF:
0.273
AC:
41526
AN:
152160
Hom.:
6315
Cov.:
33
AF XY:
0.268
AC XY:
19915
AN XY:
74406
show subpopulations
Gnomad4 AFR
AF:
0.166
Gnomad4 AMR
AF:
0.344
Gnomad4 ASJ
AF:
0.262
Gnomad4 EAS
AF:
0.0648
Gnomad4 SAS
AF:
0.174
Gnomad4 FIN
AF:
0.234
Gnomad4 NFE
AF:
0.352
Gnomad4 OTH
AF:
0.277
Alfa
AF:
0.307
Hom.:
1038
Bravo
AF:
0.277
Asia WGS
AF:
0.124
AC:
431
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.64
Cadd
Benign
12
Dann
Benign
0.81

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: rs2069840; hg19: chr7-22768572; COSMIC: COSV51733989; COSMIC: COSV51733989; API