rs8178561
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Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_000628.5(IL10RB):c.*135G>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 0.0582 in 850,424 control chromosomes in the GnomAD database, including 1,893 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.079 ( 642 hom., cov: 32)
Exomes 𝑓: 0.054 ( 1251 hom. )
Consequence
IL10RB
NM_000628.5 3_prime_UTR
NM_000628.5 3_prime_UTR
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.190
Genes affected
IL10RB (HGNC:5965): (interleukin 10 receptor subunit beta) The protein encoded by this gene belongs to the cytokine receptor family. It is an accessory chain essential for the active interleukin 10 receptor complex. Coexpression of this and IL10RA proteins has been shown to be required for IL10-induced signal transduction. This gene and three other interferon receptor genes, IFAR2, IFNAR1, and IFNGR2, form a class II cytokine receptor gene cluster located in a small region on chromosome 21. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -20 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.9).
BP6
Variant 21-33296492-G-A is Benign according to our data. Variant chr21-33296492-G-A is described in ClinVar as [Benign]. Clinvar id is 339699.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.138 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
IL10RB | NM_000628.5 | c.*135G>A | 3_prime_UTR_variant | 7/7 | ENST00000290200.7 | NP_000619.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
IL10RB | ENST00000290200.7 | c.*135G>A | 3_prime_UTR_variant | 7/7 | 1 | NM_000628.5 | ENSP00000290200.2 | |||
IFNAR2-IL10RB | ENST00000433395.7 | c.*135G>A | 3_prime_UTR_variant | 13/13 | 5 | ENSP00000388223.3 |
Frequencies
GnomAD3 genomes AF: 0.0788 AC: 11982AN: 152092Hom.: 635 Cov.: 32
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GnomAD3 exomes AF: 0.0483 AC: 6733AN: 139398Hom.: 244 AF XY: 0.0452 AC XY: 3421AN XY: 75722
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GnomAD4 exome AF: 0.0536 AC: 37454AN: 698214Hom.: 1251 Cov.: 9 AF XY: 0.0508 AC XY: 18776AN XY: 369298
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GnomAD4 genome AF: 0.0789 AC: 12015AN: 152210Hom.: 642 Cov.: 32 AF XY: 0.0776 AC XY: 5772AN XY: 74418
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ClinVar
Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
Inflammatory bowel disease 25 Benign:1
Benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jan 13, 2018 | This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. - |
not provided Benign:1
Benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
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