1-67240043-A-G

Variant summary

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

The NM_144701.3(IL23R):​c.1046-136A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.879 in 703,526 control chromosomes in the GnomAD database, including 272,305 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 0.86 ( 55963 hom., cov: 33)
Exomes 𝑓: 0.88 ( 216342 hom. )

Consequence

IL23R
NM_144701.3 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0830
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=-0.92).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.964 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
IL23RNM_144701.3 linkc.1046-136A>G intron_variant Intron 8 of 10 ENST00000347310.10 NP_653302.2 Q5VWK5-1
IL23RXM_011540790.4 linkc.1046-136A>G intron_variant Intron 8 of 10 XP_011539092.1 Q5VWK5-1
IL23RXM_011540791.4 linkc.1046-136A>G intron_variant Intron 8 of 10 XP_011539093.1 Q5VWK5-1
IL23RXM_047447227.1 linkc.1046-136A>G intron_variant Intron 8 of 10 XP_047303183.1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
IL23RENST00000347310.10 linkc.1046-136A>G intron_variant Intron 8 of 10 1 NM_144701.3 ENSP00000321345.5 Q5VWK5-1

Frequencies

GnomAD3 genomes
AF:
0.856
AC:
130163
AN:
152104
Hom.:
55921
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.794
Gnomad AMI
AF:
0.920
Gnomad AMR
AF:
0.871
Gnomad ASJ
AF:
0.907
Gnomad EAS
AF:
0.987
Gnomad SAS
AF:
0.938
Gnomad FIN
AF:
0.851
Gnomad MID
AF:
0.867
Gnomad NFE
AF:
0.871
Gnomad OTH
AF:
0.854
GnomAD4 exome
AF:
0.885
AC:
487805
AN:
551304
Hom.:
216342
AF XY:
0.888
AC XY:
263571
AN XY:
296968
show subpopulations
Gnomad4 AFR exome
AF:
0.796
Gnomad4 AMR exome
AF:
0.904
Gnomad4 ASJ exome
AF:
0.903
Gnomad4 EAS exome
AF:
0.987
Gnomad4 SAS exome
AF:
0.934
Gnomad4 FIN exome
AF:
0.836
Gnomad4 NFE exome
AF:
0.873
Gnomad4 OTH exome
AF:
0.879
GnomAD4 genome
AF:
0.856
AC:
130261
AN:
152222
Hom.:
55963
Cov.:
33
AF XY:
0.857
AC XY:
63764
AN XY:
74408
show subpopulations
Gnomad4 AFR
AF:
0.794
Gnomad4 AMR
AF:
0.871
Gnomad4 ASJ
AF:
0.907
Gnomad4 EAS
AF:
0.987
Gnomad4 SAS
AF:
0.937
Gnomad4 FIN
AF:
0.851
Gnomad4 NFE
AF:
0.871
Gnomad4 OTH
AF:
0.855
Alfa
AF:
0.864
Hom.:
9886
Bravo
AF:
0.854
Asia WGS
AF:
0.960
AC:
3341
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.92
CADD
Benign
3.3
DANN
Benign
0.45

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.060
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: rs10889671; hg19: chr1-67705726; API