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GeneBe

rs1004819

Variant summary

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

The NM_144701.3(IL23R):c.653-2380G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.309 in 151,990 control chromosomes in the GnomAD database, including 7,724 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 0.31 ( 7724 hom., cov: 32)

Consequence

IL23R
NM_144701.3 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.372
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=-0.9).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.557 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
IL23RNM_144701.3 linkuse as main transcriptc.653-2380G>A intron_variant ENST00000347310.10
IL23RXM_011540790.4 linkuse as main transcriptc.653-2380G>A intron_variant
IL23RXM_011540791.4 linkuse as main transcriptc.653-2380G>A intron_variant
IL23RXM_047447227.1 linkuse as main transcriptc.653-2380G>A intron_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
IL23RENST00000347310.10 linkuse as main transcriptc.653-2380G>A intron_variant 1 NM_144701.3 P1Q5VWK5-1

Frequencies

GnomAD3 genomes
AF:
0.309
AC:
46884
AN:
151872
Hom.:
7718
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.297
Gnomad AMI
AF:
0.331
Gnomad AMR
AF:
0.247
Gnomad ASJ
AF:
0.342
Gnomad EAS
AF:
0.574
Gnomad SAS
AF:
0.565
Gnomad FIN
AF:
0.263
Gnomad MID
AF:
0.446
Gnomad NFE
AF:
0.296
Gnomad OTH
AF:
0.311
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.309
AC:
46909
AN:
151990
Hom.:
7724
Cov.:
32
AF XY:
0.311
AC XY:
23114
AN XY:
74300
show subpopulations
Gnomad4 AFR
AF:
0.297
Gnomad4 AMR
AF:
0.246
Gnomad4 ASJ
AF:
0.342
Gnomad4 EAS
AF:
0.574
Gnomad4 SAS
AF:
0.566
Gnomad4 FIN
AF:
0.263
Gnomad4 NFE
AF:
0.296
Gnomad4 OTH
AF:
0.311
Alfa
AF:
0.306
Hom.:
10965
Bravo
AF:
0.302
Asia WGS
AF:
0.500
AC:
1737
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.90
Cadd
Benign
1.1
Dann
Benign
0.41

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: rs1004819; hg19: chr1-67670213; API