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GeneBe

rs2201841

Variant summary

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

The NM_144701.3(IL23R):c.956-8194A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.285 in 151,464 control chromosomes in the GnomAD database, including 7,312 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 0.29 ( 7312 hom., cov: 29)

Consequence

IL23R
NM_144701.3 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.347
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]
C1orf141 (HGNC:32044): (chromosome 1 open reading frame 141)

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=-0.79).
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.956-8194A>G intron_variant ENST00000347310.10
IL23RXM_011540790.4 linkuse as main transcriptc.956-8194A>G intron_variant
IL23RXM_011540791.4 linkuse as main transcriptc.956-8194A>G intron_variant
IL23RXM_047447227.1 linkuse as main transcriptc.956-8194A>G intron_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
IL23RENST00000347310.10 linkuse as main transcriptc.956-8194A>G intron_variant 1 NM_144701.3 P1Q5VWK5-1

Frequencies

GnomAD3 genomes
AF:
0.285
AC:
43206
AN:
151346
Hom.:
7304
Cov.:
29
show subpopulations
Gnomad AFR
AF:
0.163
Gnomad AMI
AF:
0.310
Gnomad AMR
AF:
0.266
Gnomad ASJ
AF:
0.338
Gnomad EAS
AF:
0.724
Gnomad SAS
AF:
0.585
Gnomad FIN
AF:
0.294
Gnomad MID
AF:
0.446
Gnomad NFE
AF:
0.304
Gnomad OTH
AF:
0.308
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.285
AC:
43236
AN:
151464
Hom.:
7312
Cov.:
29
AF XY:
0.292
AC XY:
21573
AN XY:
74000
show subpopulations
Gnomad4 AFR
AF:
0.164
Gnomad4 AMR
AF:
0.266
Gnomad4 ASJ
AF:
0.338
Gnomad4 EAS
AF:
0.724
Gnomad4 SAS
AF:
0.587
Gnomad4 FIN
AF:
0.294
Gnomad4 NFE
AF:
0.304
Gnomad4 OTH
AF:
0.311
Alfa
AF:
0.319
Hom.:
18263
Bravo
AF:
0.275
Asia WGS
AF:
0.579
AC:
2007
AN:
3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.79
Cadd
Benign
5.7
Dann
Benign
0.78

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: rs2201841; hg19: chr1-67694202; API