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rs7278931

Positions:

Variant summary

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

The NM_001405850.1(IL10RB):​c.805-8043G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.224 in 152,052 control chromosomes in the GnomAD database, including 4,000 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 ( 4000 hom., cov: 32)

Consequence

IL10RB
NM_001405850.1 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.237
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 = 0.373 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
IL10RBNM_001405849.1 linkuse as main transcriptc.805-8834G>A intron_variant
IL10RBNM_001405850.1 linkuse as main transcriptc.805-8043G>A intron_variant
IL10RBNR_175973.1 linkuse as main transcriptn.746-8834G>A intron_variant, non_coding_transcript_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
IL10RBENST00000609556.3 linkuse as main transcriptc.805-8043G>A intron_variant 5 A2
IL10RBENST00000637650.2 linkuse as main transcriptc.805-8834G>A intron_variant 5 A2

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.224
AC:
34085
AN:
151934
Hom.:
3996
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.273
Gnomad AMI
AF:
0.216
Gnomad AMR
AF:
0.187
Gnomad ASJ
AF:
0.124
Gnomad EAS
AF:
0.388
Gnomad SAS
AF:
0.244
Gnomad FIN
AF:
0.253
Gnomad MID
AF:
0.120
Gnomad NFE
AF:
0.191
Gnomad OTH
AF:
0.206
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:
0.224
AC:
34107
AN:
152052
Hom.:
4000
Cov.:
32
AF XY:
0.226
AC XY:
16788
AN XY:
74324
show subpopulations
Gnomad4 AFR
AF:
0.273
Gnomad4 AMR
AF:
0.187
Gnomad4 ASJ
AF:
0.124
Gnomad4 EAS
AF:
0.387
Gnomad4 SAS
AF:
0.244
Gnomad4 FIN
AF:
0.253
Gnomad4 NFE
AF:
0.191
Gnomad4 OTH
AF:
0.203
Alfa
AF:
0.214
Hom.:
432
Bravo
AF:
0.223
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
4.0
DANN
Benign
0.79

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: rs7278931; hg19: chr21-34672447; API