chr7-22727026-C-G
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NR_131935.1(IL6-AS1):n.54-321G>C variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.67 in 554,376 control chromosomes in the GnomAD database, including 131,638 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as other,risk factor (no stars).
Frequency
Genomes: 𝑓 0.72 ( 41246 hom., cov: 29)
Exomes 𝑓: 0.65 ( 90392 hom. )
Consequence
IL6-AS1
NR_131935.1 intron, non_coding_transcript
NR_131935.1 intron, non_coding_transcript
Scores
2
Clinical Significance
Conservation
PhyloP100: 3.25
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=-0.63).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.975 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
IL6-AS1 | NR_131935.1 | n.54-321G>C | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
IL6-AS1 | ENST00000325042.2 | n.54-321G>C | intron_variant, non_coding_transcript_variant | 1 | |||||
IL6 | ENST00000404625.5 | c.-84-153C>G | intron_variant | 5 | P1 | ||||
STEAP1B | ENST00000650428.1 | n.46+542G>C | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes AF: 0.716 AC: 108695AN: 151800Hom.: 41177 Cov.: 29
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GnomAD4 exome AF: 0.652 AC: 262377AN: 402458Hom.: 90392 AF XY: 0.661 AC XY: 139725AN XY: 211226
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GnomAD4 genome AF: 0.716 AC: 108822AN: 151918Hom.: 41246 Cov.: 29 AF XY: 0.718 AC XY: 53336AN XY: 74234
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ClinVar
Significance: other; risk factor
Submissions summary: Other:7
Revision: no assertion criteria provided
LINK: link
Submissions by phenotype
Crohn disease-associated growth failure, susceptibility to Other:1
risk factor, no assertion criteria provided | literature only | OMIM | Sep 01, 2007 | - - |
Diabetes mellitus, type 1, susceptibility to Other:1
risk factor, no assertion criteria provided | literature only | OMIM | Sep 01, 2007 | - - |
Diabetes mellitus type 2, susceptibility to Other:1
risk factor, no assertion criteria provided | literature only | OMIM | Sep 01, 2007 | - - |
INTRACRANIAL HEMORRHAGE IN BRAIN CEREBROVASCULAR MALFORMATIONS, SUSCEPTIBILITY TO Other:1
risk factor, no assertion criteria provided | literature only | OMIM | Sep 01, 2007 | - - |
Kaposi sarcoma Other:1
risk factor, no assertion criteria provided | literature only | OMIM | Sep 01, 2007 | - - |
Cholangiocarcinoma Other:1
other, no assertion criteria provided | research | Department of Surgery, Campus Charité Mitte Campus Virchow-klinikum, Charite-Universitaetsmedizin Berlin | Dec 10, 2022 | No association with disease-free or overall survival after resection of intrahepatic Cholangiocarcinoma No association with disease-free or overall survival |
RHEUMATOID ARTHRITIS, SYSTEMIC JUVENILE, SUSCEPTIBILITY TO Other:1
risk factor, no assertion criteria provided | literature only | OMIM | Sep 01, 2007 | - - |
Computational scores
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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