GeneBe

rs2508450

Variant names:

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2BP4_Strong

The NM_001558.4(IL10RA):​c.368-127T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 31)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control

Consequence

IL10RA
NM_001558.4 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.170

Publications

16 publications found
Variant links:
Genes affected
IL10RA (HGNC:5964): (interleukin 10 receptor subunit alpha) The protein encoded by this gene is a receptor for interleukin 10. This protein is structurally related to interferon receptors. It has been shown to mediate the immunosuppressive signal of interleukin 10, and thus inhibits the synthesis of proinflammatory cytokines. This receptor is reported to promote survival of progenitor myeloid cells through the insulin receptor substrate-2/PI 3-kinase/AKT pathway. Activation of this receptor leads to tyrosine phosphorylation of JAK1 and TYK2 kinases. Two transcript variants, one protein-coding and the other not protein-coding, have been found for this gene. [provided by RefSeq, Jan 2009]
IL10RA Gene-Disease associations (from GenCC):
  • inflammatory bowel disease 28
    Inheritance: AR Classification: DEFINITIVE, STRONG, MODERATE Submitted by: Ambry Genetics, ClinGen, Labcorp Genetics (formerly Invitae)
  • IL10-related early-onset inflammatory bowel disease
    Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet

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ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.7).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001558.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.
GeneTranscriptTagsHGVScHGVSpEffectExon RankProteinUniProt
IL10RA
NM_001558.4
MANE Select
c.368-127T>A
intron
N/ANP_001549.2Q13651
IL10RA
NM_001440423.1
c.-80-127T>A
intron
N/ANP_001427352.1
IL10RA
NR_026691.2
n.572-127T>A
intron
N/A

Ensembl Transcripts

Sel.
GeneTranscriptTagsHGVScHGVSpEffectExon RankProteinUniProt
IL10RA
ENST00000227752.8
TSL:1 MANE Select
c.368-127T>A
intron
N/AENSP00000227752.4Q13651
IL10RA
ENST00000529924.6
TSL:1
n.1946-127T>A
intron
N/A
IL10RA
ENST00000951964.1
c.362-127T>A
intron
N/AENSP00000622023.1

Frequencies

GnomAD3 genomes
Cov.:
31
GnomAD4 exome
Data not reliable, filtered out with message: AC0
AF:
0.00
AC:
0
AN:
670918
Hom.:
0
Cov.:
9
AF XY:
0.00
AC XY:
0
AN XY:
356536
African (AFR)
AF:
0.00
AC:
0
AN:
17678
American (AMR)
AF:
0.00
AC:
0
AN:
37936
Ashkenazi Jewish (ASJ)
AF:
0.00
AC:
0
AN:
19864
East Asian (EAS)
AF:
0.00
AC:
0
AN:
34060
South Asian (SAS)
AF:
0.00
AC:
0
AN:
65672
European-Finnish (FIN)
AF:
0.00
AC:
0
AN:
48028
Middle Eastern (MID)
AF:
0.00
AC:
0
AN:
4194
European-Non Finnish (NFE)
AF:
0.00
AC:
0
AN:
409492
Other (OTH)
AF:
0.00
AC:
0
AN:
33994
GnomAD4 genome
Cov.:
31

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.70
CADD
Benign
5.6
DANN
Benign
0.87
PhyloP100
-0.17

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

Other links and lift over

dbSNP: rs2508450; hg19: chr11-117863829; API