chr1-206768519-A-G
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Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_000572.3(IL10):c.*117T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.41 in 695,764 control chromosomes in the GnomAD database, including 64,042 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.42 ( 14000 hom., cov: 31)
Exomes 𝑓: 0.41 ( 50042 hom. )
Consequence
IL10
NM_000572.3 3_prime_UTR
NM_000572.3 3_prime_UTR
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.453
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 -14 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.61).
BP6
Variant 1-206768519-A-G is Benign according to our data. Variant chr1-206768519-A-G is described in ClinVar as [Benign]. Clinvar id is 2628225.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr1-206768519-A-G is described in Lovd as [Benign].
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.481 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
IL10 | NM_000572.3 | c.*117T>C | 3_prime_UTR_variant | 5/5 | ENST00000423557.1 | NP_000563.1 | ||
IL10 | NM_001382624.1 | c.*117T>C | 3_prime_UTR_variant | 3/3 | NP_001369553.1 | |||
IL10 | NR_168466.1 | n.951T>C | non_coding_transcript_exon_variant | 6/6 | ||||
IL10 | NR_168467.1 | n.481T>C | non_coding_transcript_exon_variant | 3/3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
IL10 | ENST00000423557.1 | c.*117T>C | 3_prime_UTR_variant | 5/5 | 1 | NM_000572.3 | ENSP00000412237 | P1 |
Frequencies
GnomAD3 genomes AF: 0.417 AC: 63370AN: 151816Hom.: 13979 Cov.: 31
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GnomAD4 exome AF: 0.408 AC: 221827AN: 543830Hom.: 50042 Cov.: 4 AF XY: 0.401 AC XY: 118071AN XY: 294534
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GnomAD4 genome AF: 0.418 AC: 63439AN: 151934Hom.: 14000 Cov.: 31 AF XY: 0.410 AC XY: 30441AN XY: 74266
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | Unidad de Genómica Garrahan, Hospital de Pediatría Garrahan | Nov 12, 2023 | This variant is classified as Benign based on local population frequency. This variant was detected in 34% of patients studied by a panel of primary immunodeficiencies. Number of patients: 33. Only high quality variants are reported. - |
Computational scores
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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