Menu
GeneBe

rs10889677

Variant summary

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

The NM_144701.3(IL23R):c.*309C>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.325 in 360,760 control chromosomes in the GnomAD database, including 22,575 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 0.28 ( 7318 hom., cov: 32)
Exomes 𝑓: 0.36 ( 15257 hom. )

Consequence

IL23R
NM_144701.3 3_prime_UTR

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.209
Variant links:
Genes affected
IL23R (HGNC:19100): (interleukin 23 receptor) The protein encoded by this gene is a subunit of the receptor for IL23A/IL23. This protein pairs with the receptor molecule IL12RB1/IL12Rbeta1, and both are required for IL23A signaling. This protein associates constitutively with Janus kinase 2 (JAK2), and also binds to transcription activator STAT3 in a ligand-dependent manner. [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=-0.77).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.705 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
IL23RNM_144701.3 linkuse as main transcriptc.*309C>A 3_prime_UTR_variant 11/11 ENST00000347310.10
IL23RXM_011540790.4 linkuse as main transcriptc.*309C>A 3_prime_UTR_variant 11/11
IL23RXM_011540791.4 linkuse as main transcriptc.*309C>A 3_prime_UTR_variant 11/11
IL23RXM_047447227.1 linkuse as main transcriptc.1239+3510C>A intron_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
IL23RENST00000347310.10 linkuse as main transcriptc.*309C>A 3_prime_UTR_variant 11/111 NM_144701.3 P1Q5VWK5-1
IL23RENST00000473881.2 linkuse as main transcriptc.*1025C>A 3_prime_UTR_variant, NMD_transcript_variant 4/41

Frequencies

GnomAD3 genomes
AF:
0.285
AC:
43213
AN:
151888
Hom.:
7310
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.159
Gnomad AMI
AF:
0.310
Gnomad AMR
AF:
0.267
Gnomad ASJ
AF:
0.344
Gnomad EAS
AF:
0.724
Gnomad SAS
AF:
0.589
Gnomad FIN
AF:
0.293
Gnomad MID
AF:
0.443
Gnomad NFE
AF:
0.304
Gnomad OTH
AF:
0.308
GnomAD4 exome
AF:
0.355
AC:
74117
AN:
208754
Hom.:
15257
Cov.:
0
AF XY:
0.373
AC XY:
41629
AN XY:
111556
show subpopulations
Gnomad4 AFR exome
AF:
0.155
Gnomad4 AMR exome
AF:
0.286
Gnomad4 ASJ exome
AF:
0.352
Gnomad4 EAS exome
AF:
0.709
Gnomad4 SAS exome
AF:
0.554
Gnomad4 FIN exome
AF:
0.272
Gnomad4 NFE exome
AF:
0.304
Gnomad4 OTH exome
AF:
0.334
GnomAD4 genome
AF:
0.284
AC:
43244
AN:
152006
Hom.:
7318
Cov.:
32
AF XY:
0.290
AC XY:
21570
AN XY:
74270
show subpopulations
Gnomad4 AFR
AF:
0.159
Gnomad4 AMR
AF:
0.267
Gnomad4 ASJ
AF:
0.344
Gnomad4 EAS
AF:
0.724
Gnomad4 SAS
AF:
0.591
Gnomad4 FIN
AF:
0.293
Gnomad4 NFE
AF:
0.304
Gnomad4 OTH
AF:
0.311
Alfa
AF:
0.321
Hom.:
17493
Bravo
AF:
0.274
Asia WGS
AF:
0.579
AC:
2007
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.77
Cadd
Benign
3.4
Dann
Benign
0.89

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: rs10889677; hg19: chr1-67725120; API