dbSNP rs2863212: IL23R:c.799-141C>T (chr1-67219433-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_144701.3(IL23R):c.799-141C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.889 in 732,406 control chromosomes in the GnomAD database, including 290,068 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 0.86 ( 56972 hom., cov: 33)

Exomes 𝑓: 0.90 ( 233096 hom. )

Consequence

IL23R
NM_144701.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0300

Publications

16 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

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=-0.97).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.964 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	MANE	Protein	UniProt
IL23R	NM_144701.3 link	c.799-141C>T	intron_variant	Intron 6 of 10	ENST00000347310.10	NP_653302.2	Q5VWK5-1
IL23R	XM_011540790.4 link	c.799-141C>T	intron_variant	Intron 6 of 10		XP_011539092.1	Q5VWK5-1
IL23R	XM_011540791.4 link	c.799-141C>T	intron_variant	Intron 6 of 10		XP_011539093.1	Q5VWK5-1
IL23R	XM_047447227.1 link	c.799-141C>T	intron_variant	Intron 6 of 10		XP_047303183.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
IL23R	ENST00000347310.10 link	c.799-141C>T		intron_variant	Intron 6 of 10	1	NM_144701.3	ENSP00000321345.5		Q5VWK5-1

Frequencies

GnomAD3 genomes

AF:

0.863

AC:

131281

AN:

152124

Hom.:

56938

Cov.:

show subpopulations

Gnomad AFR

AF:

0.783

Gnomad AMI

AF:

0.935

Gnomad AMR

AF:

0.880

Gnomad ASJ

AF:

0.920

Gnomad EAS

AF:

0.986

Gnomad SAS

AF:

0.970

Gnomad FIN

AF:

0.854

Gnomad MID

AF:

0.873

Gnomad NFE

AF:

0.888

Gnomad OTH

AF:

0.862

GnomAD4 exome

AF:

0.895

AC:

519403

AN:

580164

Hom.:

233096

AF XY:

0.899

AC XY:

278833

AN XY:

310208

show subpopulations

African (AFR)

AF:

0.777

AC:

11876

AN:

15284

American (AMR)

AF:

0.907

AC:

25160

AN:

27748

Ashkenazi Jewish (ASJ)

AF:

0.918

AC:

16386

AN:

17848

East Asian (EAS)

AF:

0.988

AC:

31839

AN:

32232

South Asian (SAS)

AF:

0.966

AC:

53871

AN:

55742

European-Finnish (FIN)

AF:

0.837

AC:

27233

AN:

32536

Middle Eastern (MID)

AF:

0.882

AC:

2117

AN:

2400

European-Non Finnish (NFE)

AF:

0.885

AC:

323320

AN:

365392

Other (OTH)

AF:

0.891

AC:

27601

AN:

30982

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.495

Heterozygous variant carriers

2723

5446

8170

10893

13616

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

2558

5116

7674

10232

12790

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.863

AC:

131371

AN:

152242

Hom.:

56972

Cov.:

AF XY:

0.864

AC XY:

64295

AN XY:

74440

show subpopulations

African (AFR)

AF:

0.783

AC:

32510

AN:

41510

American (AMR)

AF:

0.880

AC:

13461

AN:

15296

Ashkenazi Jewish (ASJ)

AF:

0.920

AC:

3191

AN:

3468

East Asian (EAS)

AF:

0.986

AC:

5121

AN:

5192

South Asian (SAS)

AF:

0.970

AC:

4685

AN:

4830

European-Finnish (FIN)

AF:

0.854

AC:

9051

AN:

10602

Middle Eastern (MID)

AF:

0.881

AC:

259

AN:

294

European-Non Finnish (NFE)

AF:

0.888

AC:

60418

AN:

68026

Other (OTH)

AF:

0.863

AC:

1824

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

916

1832

2749

3665

4581

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

898

1796

2694

3592

4490

<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:

0.886

Hom.:

92570

Bravo

AF:

0.860

Asia WGS

AF:

0.966

AC:

3359

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.97

CADD

Benign

2.8

(source)

DANN

Benign

0.77

PhyloP100

-0.030

PromoterAI

0.043

Neutral

(source)

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over