Variant rs7518660 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The NM_144701.3(IL23R):c.955+30G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.448 in 1,594,142 control chromosomes in the GnomAD database, including 163,702 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.46 ( 16500 hom., cov: 32)

Exomes 𝑓: 0.45 ( 147202 hom. )

Consequence

IL23R
NM_144701.3 intron

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -2.38

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 made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.98).

BP6

Variant 1-67219760-G-A is Benign according to our data. Variant chr1-67219760-G-A is described in ClinVar as [Benign]. Clinvar id is 2688373.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.524 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	MANE	Protein	UniProt
IL23R	NM_144701.3 link	c.955+30G>A	intron_variant	ENST00000347310.10	NP_653302.2	Q5VWK5-1
IL23R	XM_011540790.4 link	c.955+30G>A	intron_variant		XP_011539092.1	Q5VWK5-1
IL23R	XM_011540791.4 link	c.955+30G>A	intron_variant		XP_011539093.1	Q5VWK5-1
IL23R	XM_047447227.1 link	c.955+30G>A	intron_variant		XP_047303183.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
IL23R	ENST00000347310.10 link	c.955+30G>A		intron_variant		1	NM_144701.3	ENSP00000321345.5		Q5VWK5-1

Frequencies

GnomAD3 genomes

AF:

0.461

AC:

70030

AN:

151840

Hom.:

16492

Cov.:

show subpopulations

Gnomad AFR

AF:

0.489

Gnomad AMI

AF:

0.431

Gnomad AMR

AF:

0.534

Gnomad ASJ

AF:

0.428

Gnomad EAS

AF:

0.259

Gnomad SAS

AF:

0.281

Gnomad FIN

AF:

0.434

Gnomad MID

AF:

0.348

Gnomad NFE

AF:

0.464

Gnomad OTH

AF:

0.436

GnomAD3 exomes

AF:

0.434

AC:

108634

AN:

250042

Hom.:

24785

AF XY:

0.423

AC XY:

57352

AN XY:

135460

show subpopulations

Gnomad AFR exome

AF:

0.498

Gnomad AMR exome

AF:

0.578

Gnomad ASJ exome

AF:

0.416

Gnomad EAS exome

AF:

0.254

Gnomad SAS exome

AF:

0.290

Gnomad FIN exome

AF:

0.423

Gnomad NFE exome

AF:

0.454

Gnomad OTH exome

AF:

0.436

GnomAD4 exome

AF:

0.447

AC:

644302

AN:

1442182

Hom.:

147202

Cov.:

AF XY:

0.441

AC XY:

316687

AN XY:

718786

show subpopulations

Gnomad4 AFR exome

AF:

0.478

Gnomad4 AMR exome

AF:

0.568

Gnomad4 ASJ exome

AF:

0.427

Gnomad4 EAS exome

AF:

0.271

Gnomad4 SAS exome

AF:

0.289

Gnomad4 FIN exome

AF:

0.431

Gnomad4 NFE exome

AF:

0.462

Gnomad4 OTH exome

AF:

0.436

GnomAD4 genome

AF:

0.461

AC:

70079

AN:

151960

Hom.:

16500

Cov.:

AF XY:

0.457

AC XY:

33943

AN XY:

74242

show subpopulations

Gnomad4 AFR

AF:

0.488

Gnomad4 AMR

AF:

0.534

Gnomad4 ASJ

AF:

0.428

Gnomad4 EAS

AF:

0.259

Gnomad4 SAS

AF:

0.279

Gnomad4 FIN

AF:

0.434

Gnomad4 NFE

AF:

0.464

Gnomad4 OTH

AF:

0.436

Alfa

AF:

0.452

Hom.:

3844

Bravo

AF:

0.474

Asia WGS

AF:

0.333

AC:

1160

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not specified

Benign:1

Benign, criteria provided, single submitter

clinical testing

Unidad de Genómica Garrahan, Hospital de Pediatría Garrahan

Jan 24, 2024

This variant is classified as Benign based on local population frequency. This variant was detected in 73% of patients studied by a panel of primary immunodeficiencies. Number of patients: 64. Only high quality variants are reported. -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.98

CADD

Benign

0.0050

DANN

Benign

0.17

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

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

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over