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GeneBe

rs6517158

Positions:

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001405850.1(IL10RB):​c.805-8749T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.221 in 151,984 control chromosomes in the GnomAD database, including 3,868 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.22 ( 3868 hom., cov: 32)

Consequence

IL10RB
NM_001405850.1 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.53
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]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
?
    BP4 - Multiple lines of computational evidence suggest no impact on gene or gene product (conservation, evolutionary, splicing impact, etc.)
Computational evidence support a benign effect (BayesDel_noAF=-0.88).
BA1
?
    BA1 - Allele frequency is >5% in Exome Sequencing Project, 1000 Genomes Project, or Exome Aggregation Consortium
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.371 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
IL10RBNM_001405849.1 linkuse as main transcriptc.805-9540T>C intron_variant
IL10RBNM_001405850.1 linkuse as main transcriptc.805-8749T>C intron_variant
IL10RBNR_175973.1 linkuse as main transcriptn.746-9540T>C intron_variant, non_coding_transcript_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
IL10RBENST00000609556.3 linkuse as main transcriptc.805-8749T>C intron_variant 5 A2
IL10RBENST00000637650.2 linkuse as main transcriptc.805-9540T>C intron_variant 5 A2

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.221
AC:
33622
AN:
151866
Hom.:
3864
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.271
Gnomad AMI
AF:
0.215
Gnomad AMR
AF:
0.185
Gnomad ASJ
AF:
0.124
Gnomad EAS
AF:
0.386
Gnomad SAS
AF:
0.240
Gnomad FIN
AF:
0.252
Gnomad MID
AF:
0.123
Gnomad NFE
AF:
0.187
Gnomad OTH
AF:
0.202
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.221
AC:
33646
AN:
151984
Hom.:
3868
Cov.:
32
AF XY:
0.223
AC XY:
16551
AN XY:
74260
show subpopulations
Gnomad4 AFR
AF:
0.271
Gnomad4 AMR
AF:
0.185
Gnomad4 ASJ
AF:
0.124
Gnomad4 EAS
AF:
0.385
Gnomad4 SAS
AF:
0.239
Gnomad4 FIN
AF:
0.252
Gnomad4 NFE
AF:
0.187
Gnomad4 OTH
AF:
0.199
Alfa
AF:
0.211
Hom.:
418
Bravo
AF:
0.221
Asia WGS
AF:
0.353
AC:
1227
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.88
CADD
Benign
2.9
DANN
Benign
0.68

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs6517158; hg19: chr21-34671741; API