rs6697497
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_000572.3(IL10):c.*518G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0168 in 217,102 control chromosomes in the GnomAD database, including 141 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 0.022 ( 131 hom., cov: 32)
Exomes 𝑓: 0.0035 ( 10 hom. )
Consequence
IL10
NM_000572.3 3_prime_UTR
NM_000572.3 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.0260
Genes affected
IL10 (HGNC:5962): (interleukin 10) The protein encoded by this gene is a cytokine produced primarily by monocytes and to a lesser extent by lymphocytes. This cytokine has pleiotropic effects in immunoregulation and inflammation. It down-regulates the expression of Th1 cytokines, MHC class II Ags, and costimulatory molecules on macrophages. It also enhances B cell survival, proliferation, and antibody production. This cytokine can block NF-kappa B activity, and is involved in the regulation of the JAK-STAT signaling pathway. Knockout studies in mice suggested the function of this cytokine as an essential immunoregulator in the intestinal tract. Mutations in this gene are associated with an increased susceptibility to HIV-1 infection and rheumatoid arthritis. [provided by RefSeq, May 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=-0.69).
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0767 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
IL10 | NM_000572.3 | c.*518G>A | 3_prime_UTR_variant | 5/5 | ENST00000423557.1 | ||
IL10 | NM_001382624.1 | c.*518G>A | 3_prime_UTR_variant | 3/3 | |||
IL10 | NR_168466.1 | n.1352G>A | non_coding_transcript_exon_variant | 6/6 | |||
IL10 | NR_168467.1 | n.882G>A | non_coding_transcript_exon_variant | 3/3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
IL10 | ENST00000423557.1 | c.*518G>A | 3_prime_UTR_variant | 5/5 | 1 | NM_000572.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0224 AC: 3408AN: 152114Hom.: 131 Cov.: 32
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GnomAD4 exome AF: 0.00355 AC: 230AN: 64870Hom.: 10 Cov.: 0 AF XY: 0.00341 AC XY: 106AN XY: 31072
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GnomAD4 genome ? AF: 0.0224 AC: 3417AN: 152232Hom.: 131 Cov.: 32 AF XY: 0.0214 AC XY: 1593AN XY: 74442
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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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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at