dbSNP rs10489629: IL23R:c.955+2936T>C (chr1-67222666-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is . The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_144701.3(IL23R):c.955+2936T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.476 in 152,028 control chromosomes in the GnomAD database, including 17,751 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 0.48 ( 17751 hom., cov: 31)

Consequence

IL23R
NM_144701.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.28

Publications

95 publications found

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]

IL23R links:

C1orf141 (HGNC:32044): (chromosome 1 open reading frame 141)

C1orf141 links:

Genome browser will be placed here

new If you want to explore the variant's impact on the transcript NM_144701.3, check out the Mutation Effect Viewer. This is especially useful for frameshift variants or if you want to visualize the effect of exon loss / intron retention.

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.91).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.552 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_144701.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	IL23R	NM_144701.3	MANE Select	c.955+2936T>C		intron	N/A	NP_653302.2

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
IL23R	ENST00000347310.10	TSL:1 MANE Select	c.955+2936T>C	intron	N/A	ENSP00000321345.5	Q5VWK5-1
IL23R	ENST00000425614.3	TSL:1	c.190+2936T>C	intron	N/A	ENSP00000387640.2	Q5VWK5-6
IL23R	ENST00000473881.2	TSL:1	n.190+2936T>C	intron	N/A	ENSP00000486667.1	A0A0D9SFJ7

Frequencies

GnomAD3 genomes

AF:

0.476

AC:

72296

AN:

151910

Hom.:

17738

Cov.:

show subpopulations

Gnomad AFR

AF:

0.558

Gnomad AMI

AF:

0.435

Gnomad AMR

AF:

0.539

Gnomad ASJ

AF:

0.428

Gnomad EAS

AF:

0.264

Gnomad SAS

AF:

0.278

Gnomad FIN

AF:

0.413

Gnomad MID

AF:

0.380

Gnomad NFE

AF:

0.456

Gnomad OTH

AF:

0.455

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome

AF:

0.476

AC:

72357

AN:

152028

Hom.:

17751

Cov.:

AF XY:

0.470

AC XY:

34942

AN XY:

74304

show subpopulations

African (AFR)

AF:

0.558

AC:

23134

AN:

41454

American (AMR)

AF:

0.539

AC:

8236

AN:

15266

Ashkenazi Jewish (ASJ)

AF:

0.428

AC:

1485

AN:

3466

East Asian (EAS)

AF:

0.264

AC:

1366

AN:

5176

South Asian (SAS)

AF:

0.277

AC:

1334

AN:

4824

European-Finnish (FIN)

AF:

0.413

AC:

4365

AN:

10564

Middle Eastern (MID)

AF:

0.384

AC:

113

AN:

294

European-Non Finnish (NFE)

AF:

0.456

AC:

30970

AN:

67968

Other (OTH)

AF:

0.455

AC:

960

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1888

3775

5663

7550

9438

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

650

1300

1950

2600

3250

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.464

Hom.:

53324

Bravo

AF:

0.493

Asia WGS

AF:

0.344

AC:

1198

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

0.60

(source)

DANN

Benign

0.51

PhyloP100

-1.3

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over