rs4655683

Variant summary

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

The ENST00000637002.1(IL23R):​c.-30+6769G>A variant causes a intron, NMD transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.374 in 151,988 control chromosomes in the GnomAD database, including 10,807 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 0.37 ( 10807 hom., cov: 32)

Consequence

IL23R
ENST00000637002.1 intron, NMD_transcript

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.293
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=-1.01).
BA1
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.471 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
IL23RXM_011540790.4 linkuse as main transcriptc.-30+6769G>A intron_variant XP_011539092.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
IL23RENST00000637002.1 linkuse as main transcriptc.-30+6769G>A intron_variant, NMD_transcript_variant 1 ENSP00000490340
C1orf141ENST00000371007.6 linkuse as main transcriptc.-103-14703C>T intron_variant 5 ENSP00000360046 P1Q5JVX7-1
C1orf141ENST00000448166.6 linkuse as main transcriptc.-103-14703C>T intron_variant 5 ENSP00000415519
IL23RENST00000697222.1 linkuse as main transcriptc.-30+6769G>A intron_variant ENSP00000513189

Frequencies

GnomAD3 genomes
AF:
0.373
AC:
56711
AN:
151870
Hom.:
10780
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.412
Gnomad AMI
AF:
0.225
Gnomad AMR
AF:
0.480
Gnomad ASJ
AF:
0.253
Gnomad EAS
AF:
0.374
Gnomad SAS
AF:
0.323
Gnomad FIN
AF:
0.345
Gnomad MID
AF:
0.244
Gnomad NFE
AF:
0.342
Gnomad OTH
AF:
0.379
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.374
AC:
56789
AN:
151988
Hom.:
10807
Cov.:
32
AF XY:
0.374
AC XY:
27803
AN XY:
74292
show subpopulations
Gnomad4 AFR
AF:
0.413
Gnomad4 AMR
AF:
0.480
Gnomad4 ASJ
AF:
0.253
Gnomad4 EAS
AF:
0.373
Gnomad4 SAS
AF:
0.322
Gnomad4 FIN
AF:
0.345
Gnomad4 NFE
AF:
0.342
Gnomad4 OTH
AF:
0.381
Alfa
AF:
0.351
Hom.:
13228
Bravo
AF:
0.387
Asia WGS
AF:
0.409
AC:
1420
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-1.0
CADD
Benign
1.3
DANN
Benign
0.64

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: rs4655683; hg19: chr1-67611613; API