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GeneBe

rs10889677

Variant summary

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

The NM_144701(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 0.285 in 151888 control chromosomes in the gnomAD Genomes database, including 7310 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 ( 7310 hom., cov: 32)

Consequence

IL23R
NM_144701 3_prime_UTR

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.209

Links

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
?
GnomAd highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.704 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
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
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
2.4
Dann
Benign
0.89

Splicing

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;