NM_000628.5:c.647-754_647-751dupGTTT
Variant summary
Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BA1
The NM_000628.5(IL10RB):c.647-754_647-751dupGTTT variant causes a intron change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.51 ( 20561 hom., cov: 0)
Consequence
IL10RB
NM_000628.5 intron
NM_000628.5 intron
Scores
Not classified
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.244
Publications
2 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]
IL10RB Gene-Disease associations (from GenCC):
- inflammatory bowel disease 25Inheritance: AR Classification: STRONG Submitted by: Labcorp Genetics (formerly Invitae)
- IL10-related early-onset inflammatory bowel diseaseInheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet
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ACMG classification
Classification was made for transcript
Our verdict: Benign. The variant received -8 ACMG points.
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.687 is higher than 0.05.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
IL10RB | ENST00000290200.7 | c.647-763_647-762insGTTT | intron_variant | Intron 5 of 6 | 1 | NM_000628.5 | ENSP00000290200.2 | |||
IFNAR2-IL10RB | ENST00000433395.7 | c.1307-763_1307-762insGTTT | intron_variant | Intron 11 of 12 | 5 | ENSP00000388223.3 |
Frequencies
GnomAD3 genomes AF: 0.507 AC: 76458AN: 150756Hom.: 20525 Cov.: 0 show subpopulations
GnomAD3 genomes
AF:
AC:
76458
AN:
150756
Hom.:
Cov.:
0
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.507 AC: 76533AN: 150872Hom.: 20561 Cov.: 0 AF XY: 0.502 AC XY: 37028AN XY: 73710 show subpopulations
GnomAD4 genome
AF:
AC:
76533
AN:
150872
Hom.:
Cov.:
0
AF XY:
AC XY:
37028
AN XY:
73710
show subpopulations
African (AFR)
AF:
AC:
28378
AN:
40922
American (AMR)
AF:
AC:
6191
AN:
15198
Ashkenazi Jewish (ASJ)
AF:
AC:
1931
AN:
3462
East Asian (EAS)
AF:
AC:
1061
AN:
5138
South Asian (SAS)
AF:
AC:
1784
AN:
4776
European-Finnish (FIN)
AF:
AC:
4871
AN:
10382
Middle Eastern (MID)
AF:
AC:
129
AN:
292
European-Non Finnish (NFE)
AF:
AC:
30739
AN:
67694
Other (OTH)
AF:
AC:
1014
AN:
2102
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.499
Heterozygous variant carriers
0
1711
3421
5132
6842
8553
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Genome Het
Genome Hom
Variant carriers
0
650
1300
1950
2600
3250
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
Alfa
AF:
Hom.:
Asia WGS
AF:
AC:
950
AN:
3478
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
PhyloP100
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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