Genetic Variant IL23R:n.*1025C>A (chr1-67259437-C-A) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000473881.2(IL23R):n.*1025C>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.325 in 360,760 control chromosomes in the GnomAD database, including 22,575 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 ( 7318 hom., cov: 32)

Exomes 𝑓: 0.36 ( 15257 hom. )

Consequence

IL23R
ENST00000473881.2 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.209

Publications

223 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:

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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=-0.77).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.705 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	MANE	Protein	UniProt
IL23R	NM_144701.3 link	c.*309C>A	3_prime_UTR_variant	Exon 11 of 11	ENST00000347310.10	NP_653302.2	Q5VWK5-1
IL23R	XM_011540790.4 link	c.*309C>A	3_prime_UTR_variant	Exon 11 of 11		XP_011539092.1	Q5VWK5-1
IL23R	XM_011540791.4 link	c.*309C>A	3_prime_UTR_variant	Exon 11 of 11		XP_011539093.1	Q5VWK5-1
IL23R	XM_047447227.1 link	c.1239+3510C>A	intron_variant	Intron 10 of 10		XP_047303183.1

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
IL23R	ENST00000473881.2 link	n.*1025C>A	non_coding_transcript_exon_variant	Exon 4 of 4	1		ENSP00000486667.1	A0A0D9SFJ7
IL23R	ENST00000347310.10 link	c.*309C>A	3_prime_UTR_variant	Exon 11 of 11	1	NM_144701.3	ENSP00000321345.5	Q5VWK5-1
IL23R	ENST00000473881.2 link	n.*1025C>A	3_prime_UTR_variant	Exon 4 of 4	1		ENSP00000486667.1	A0A0D9SFJ7
IL23R	ENST00000425614.3 link	c.*309C>A	downstream_gene_variant		1		ENSP00000387640.2	Q5VWK5-6

Frequencies

GnomAD3 genomes

AF:

0.285

AC:

43213

AN:

151888

Hom.:

7310

Cov.:

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

Cov.:

AF XY:

0.373

AC XY:

41629

AN XY:

111556

show subpopulations

African (AFR)

AF:

0.155

AC:

987

AN:

6360

American (AMR)

AF:

0.286

AC:

2148

AN:

7502

Ashkenazi Jewish (ASJ)

AF:

0.352

AC:

2070

AN:

5880

East Asian (EAS)

AF:

0.709

AC:

7508

AN:

10588

South Asian (SAS)

AF:

0.554

AC:

15608

AN:

28150

European-Finnish (FIN)

AF:

0.272

AC:

2759

AN:

10160

Middle Eastern (MID)

AF:

0.422

AC:

357

AN:

846

European-Non Finnish (NFE)

AF:

0.304

AC:

38854

AN:

127828

Other (OTH)

AF:

0.334

AC:

3826

AN:

11440

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

2086

4172

6258

8344

10430

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

326

652

978

1304

1630

<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:

0.284

AC:

43244

AN:

152006

Hom.:

7318

Cov.:

AF XY:

0.290

AC XY:

21570

AN XY:

74270

show subpopulations

African (AFR)

AF:

0.159

AC:

6605

AN:

41484

American (AMR)

AF:

0.267

AC:

4071

AN:

15268

Ashkenazi Jewish (ASJ)

AF:

0.344

AC:

1195

AN:

3470

East Asian (EAS)

AF:

0.724

AC:

3727

AN:

5148

South Asian (SAS)

AF:

0.591

AC:

2836

AN:

4802

European-Finnish (FIN)

AF:

0.293

AC:

3096

AN:

10562

Middle Eastern (MID)

AF:

0.442

AC:

129

AN:

292

European-Non Finnish (NFE)

AF:

0.304

AC:

20646

AN:

67956

Other (OTH)

AF:

0.311

AC:

657

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

1432

2865

4297

5730

7162

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

466

932

1398

1864

2330

<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:

0.307

Hom.:

31801

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

3.4

(source)

DANN

Benign

0.89

PhyloP100

-0.21

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