chr21-33266504-G-A
Variant names:
Variant summary
Our verdict is Likely benign. The variant received -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7
The NM_000628.5(IL10RB):c.39G>A(p.Leu13Leu) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000719 in 1,390,718 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: not found (cov: 32)
Exomes 𝑓: 7.2e-7 ( 0 hom. )
Consequence
IL10RB
NM_000628.5 synonymous
NM_000628.5 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -1.15
Publications
0 publications found
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 was made for transcript
Our verdict: Likely_benign. The variant received -5 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.54).
BP6
Variant 21-33266504-G-A is Benign according to our data. Variant chr21-33266504-G-A is described in ClinVar as Likely_benign. ClinVar VariationId is 1643363.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=-1.15 with no splicing effect.
Variant Effect in Transcripts
ACMG analysis was done for transcript: NM_000628.5. You can select a different transcript below to see updated ACMG assignments.
RefSeq Transcripts
| Sel. | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| IL10RB | NM_000628.5 | MANE Select | c.39G>A | p.Leu13Leu | synonymous | Exon 1 of 7 | NP_000619.3 | ||
| IL10RB | NM_001405850.1 | c.39G>A | p.Leu13Leu | synonymous | Exon 1 of 7 | NP_001392779.1 | A0A1B0GU52 | ||
| IL10RB | NM_001405849.1 | c.39G>A | p.Leu13Leu | synonymous | Exon 1 of 7 | NP_001392778.1 | A0A1B0GTI5 |
Ensembl Transcripts
| Sel. | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| IL10RB | ENST00000290200.7 | TSL:1 MANE Select | c.39G>A | p.Leu13Leu | synonymous | Exon 1 of 7 | ENSP00000290200.2 | Q08334 | |
| IFNAR2-IL10RB | ENST00000433395.7 | TSL:5 | c.710-1890G>A | intron | N/A | ENSP00000388223.3 | H0Y3Z8 | ||
| IL10RB | ENST00000896213.1 | c.39G>A | p.Leu13Leu | synonymous | Exon 1 of 7 | ENSP00000566272.1 |
Frequencies
GnomAD3 genomes
GnomAD3 genomes
Cov.:
32
GnomAD4 exome AF: 7.19e-7 AC: 1AN: 1390718Hom.: 0 Cov.: 31 AF XY: 0.00000146 AC XY: 1AN XY: 686496 show subpopulations
GnomAD4 exome
AF:
AC:
1
AN:
1390718
Hom.:
Cov.:
31
AF XY:
AC XY:
1
AN XY:
686496
show subpopulations
African (AFR)
AF:
AC:
0
AN:
31614
American (AMR)
AF:
AC:
0
AN:
35844
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
25178
East Asian (EAS)
AF:
AC:
0
AN:
35938
South Asian (SAS)
AF:
AC:
0
AN:
79264
European-Finnish (FIN)
AF:
AC:
0
AN:
41052
Middle Eastern (MID)
AF:
AC:
0
AN:
4552
European-Non Finnish (NFE)
AF:
AC:
0
AN:
1079412
Other (OTH)
AF:
AC:
1
AN:
57864
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.475
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
GnomAD4 genome
GnomAD4 genome
Cov.:
32
Alfa
AF:
Hom.:
ClinVar
ClinVar submissions
View on ClinVar Significance:Likely benign
Revision:criteria provided, single submitter
Pathogenic
VUS
Benign
Condition
-
-
1
Inflammatory bowel disease 25 (1)
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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