21-33268483-A-G
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_000628.5(IL10RB):c.139A>G(p.Lys47Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.275 in 1,613,124 control chromosomes in the GnomAD database, including 66,866 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_000628.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
IL10RB | ENST00000290200.7 | c.139A>G | p.Lys47Glu | missense_variant | Exon 2 of 7 | 1 | NM_000628.5 | ENSP00000290200.2 | ||
IFNAR2-IL10RB | ENST00000433395.7 | c.799A>G | p.Lys267Glu | missense_variant | Exon 8 of 13 | 5 | ENSP00000388223.3 |
Frequencies
GnomAD3 genomes AF: 0.254 AC: 38639AN: 152118Hom.: 5821 Cov.: 32
GnomAD3 exomes AF: 0.330 AC: 83064AN: 251442Hom.: 15733 AF XY: 0.330 AC XY: 44818AN XY: 135904
GnomAD4 exome AF: 0.278 AC: 405506AN: 1460888Hom.: 61045 Cov.: 33 AF XY: 0.281 AC XY: 204127AN XY: 726848
GnomAD4 genome AF: 0.254 AC: 38649AN: 152236Hom.: 5821 Cov.: 32 AF XY: 0.263 AC XY: 19580AN XY: 74422
ClinVar
Submissions by phenotype
not specified Benign:4
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This variant is classified as Benign based on local population frequency. This variant was detected in 75% of patients studied by a panel of primary immunodeficiencies. Number of patients: 72. Only high quality variants are reported. -
Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: Frequency, associated with susceptibility to hepatitis -
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Inflammatory bowel disease 25 Benign:2
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. -
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not provided Benign:1
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Hepatitis B virus, susceptibility to Other:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at