rs2069839
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Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_000600.5(IL6):c.324+70G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000963 in 845,136 control chromosomes in the GnomAD database, including 6 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 0.0032 ( 3 hom., cov: 32)
Exomes 𝑓: 0.00047 ( 3 hom. )
Consequence
IL6
NM_000600.5 intron
NM_000600.5 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.345
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 -8 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.91).
BS2
?
High AC in GnomAd4 at 490 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
IL6 | NM_000600.5 | c.324+70G>A | intron_variant | ENST00000258743.10 | |||
IL6 | NM_001318095.2 | c.96+70G>A | intron_variant | ||||
IL6 | NM_001371096.1 | c.255+70G>A | intron_variant | ||||
IL6 | XM_005249745.6 | c.486+70G>A | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
IL6 | ENST00000258743.10 | c.324+70G>A | intron_variant | 1 | NM_000600.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00321 AC: 489AN: 152196Hom.: 3 Cov.: 32
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GnomAD4 exome AF: 0.000468 AC: 324AN: 692822Hom.: 3 AF XY: 0.000372 AC XY: 138AN XY: 371100
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GnomAD4 genome ? AF: 0.00322 AC: 490AN: 152314Hom.: 3 Cov.: 32 AF XY: 0.00297 AC XY: 221AN XY: 74482
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ClinVar
Not reported inComputational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at