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

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.244

Publications

2 publications found
Variant links:
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 25
    Inheritance: AR Classification: STRONG Submitted by: Labcorp Genetics (formerly Invitae)
  • IL10-related early-onset inflammatory bowel disease
    Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet

Genome browser will be placed here

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

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
IL10RBNM_000628.5 linkc.647-754_647-751dupGTTT intron_variant Intron 5 of 6 ENST00000290200.7 NP_000619.3 Q08334

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
IL10RBENST00000290200.7 linkc.647-763_647-762insGTTT intron_variant Intron 5 of 6 1 NM_000628.5 ENSP00000290200.2 Q08334
IFNAR2-IL10RBENST00000433395.7 linkc.1307-763_1307-762insGTTT intron_variant Intron 11 of 12 5 ENSP00000388223.3 H0Y3Z8

Frequencies

GnomAD3 genomes
AF:
0.507
AC:
76458
AN:
150756
Hom.:
20525
Cov.:
0
show subpopulations
Gnomad AFR
AF:
0.693
Gnomad AMI
AF:
0.480
Gnomad AMR
AF:
0.408
Gnomad ASJ
AF:
0.558
Gnomad EAS
AF:
0.206
Gnomad SAS
AF:
0.374
Gnomad FIN
AF:
0.469
Gnomad MID
AF:
0.436
Gnomad NFE
AF:
0.454
Gnomad OTH
AF:
0.488
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.507
AC:
76533
AN:
150872
Hom.:
20561
Cov.:
0
AF XY:
0.502
AC XY:
37028
AN XY:
73710
show subpopulations
African (AFR)
AF:
0.693
AC:
28378
AN:
40922
American (AMR)
AF:
0.407
AC:
6191
AN:
15198
Ashkenazi Jewish (ASJ)
AF:
0.558
AC:
1931
AN:
3462
East Asian (EAS)
AF:
0.207
AC:
1061
AN:
5138
South Asian (SAS)
AF:
0.374
AC:
1784
AN:
4776
European-Finnish (FIN)
AF:
0.469
AC:
4871
AN:
10382
Middle Eastern (MID)
AF:
0.442
AC:
129
AN:
292
European-Non Finnish (NFE)
AF:
0.454
AC:
30739
AN:
67694
Other (OTH)
AF:
0.482
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:
0.305
Hom.:
606
Asia WGS
AF:
0.273
AC:
950
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
PhyloP100
-0.24
Mutation Taster
=100/0
polymorphism (auto)

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

Other links and lift over

dbSNP: rs1610997; hg19: chr21-34659646; API