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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(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 151346 control chromosomes in the gnomAD Genomes database, including 7304 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 ( 7304 hom., cov: 29)

Consequence

IL23R
NM_144701 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.347

Links

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.79).
BA1
?
GnomAd 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
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
8.0
Dann
Benign
0.78

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: rs2201841; hg19: chr1-67694202;