rs2243498

Variant summary

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

The NM_000628.5(IL10RB):​c.498+1443G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.48 in 152,096 control chromosomes in the GnomAD database, including 18,221 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 0.48 ( 18221 hom., cov: 32)

Consequence

IL10RB
NM_000628.5 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.675
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.87).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.611 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
IL10RBNM_000628.5 linkuse as main transcriptc.498+1443G>A intron_variant ENST00000290200.7
IFNAR2-IL10RBNM_001414505.1 linkuse as main transcriptc.1158+1443G>A intron_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
IL10RBENST00000290200.7 linkuse as main transcriptc.498+1443G>A intron_variant 1 NM_000628.5 P2

Frequencies

GnomAD3 genomes
AF:
0.480
AC:
72895
AN:
151978
Hom.:
18193
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.617
Gnomad AMI
AF:
0.313
Gnomad AMR
AF:
0.392
Gnomad ASJ
AF:
0.528
Gnomad EAS
AF:
0.202
Gnomad SAS
AF:
0.365
Gnomad FIN
AF:
0.477
Gnomad MID
AF:
0.424
Gnomad NFE
AF:
0.447
Gnomad OTH
AF:
0.455
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.480
AC:
72964
AN:
152096
Hom.:
18221
Cov.:
32
AF XY:
0.475
AC XY:
35364
AN XY:
74380
show subpopulations
Gnomad4 AFR
AF:
0.617
Gnomad4 AMR
AF:
0.391
Gnomad4 ASJ
AF:
0.528
Gnomad4 EAS
AF:
0.202
Gnomad4 SAS
AF:
0.365
Gnomad4 FIN
AF:
0.477
Gnomad4 NFE
AF:
0.447
Gnomad4 OTH
AF:
0.450
Alfa
AF:
0.467
Hom.:
2509
Bravo
AF:
0.477
Asia WGS
AF:
0.262
AC:
909
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.87
CADD
Benign
1.5
DANN
Benign
0.39

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

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: rs2243498; hg19: chr21-34653666; API