Variant rs7539625 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.798+27G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.318 in 1,608,758 control chromosomes in the GnomAD database, including 87,116 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.30 ( 7447 hom., cov: 31)

Exomes 𝑓: 0.32 ( 79669 hom. )

Consequence

IL23R
NM_144701.3 intron

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.0500

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=-0.8).

BP6

Variant 1-67207082-G-A is Benign according to our data. Variant chr1-67207082-G-A is described in ClinVar as [Benign]. Clinvar id is 2688442.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.547 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	MANE	Protein
IL23R	NM_144701.3 linkuse as main transcript	c.798+27G>A	intron_variant	ENST00000347310.10	NP_653302.2
IL23R	XM_011540790.4 linkuse as main transcript	c.798+27G>A	intron_variant		XP_011539092.1
IL23R	XM_011540791.4 linkuse as main transcript	c.798+27G>A	intron_variant		XP_011539093.1
IL23R	XM_047447227.1 linkuse as main transcript	c.798+27G>A	intron_variant		XP_047303183.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
IL23R	ENST00000347310.10 linkuse as main transcript	c.798+27G>A		intron_variant		1	NM_144701.3	ENSP00000321345	P1	Q5VWK5-1

Frequencies

GnomAD3 genomes

AF:

0.303

AC:

45978

AN:

151852

Hom.:

7442

Cov.:

show subpopulations

Gnomad AFR

AF:

0.296

Gnomad AMI

AF:

0.329

Gnomad AMR

AF:

0.211

Gnomad ASJ

AF:

0.328

Gnomad EAS

AF:

0.531

Gnomad SAS

AF:

0.564

Gnomad FIN

AF:

0.263

Gnomad MID

AF:

0.449

Gnomad NFE

AF:

0.295

Gnomad OTH

AF:

0.302

GnomAD3 exomes

AF:

0.326

AC:

81869

AN:

250800

Hom.:

15322

AF XY:

0.343

AC XY:

46505

AN XY:

135644

show subpopulations

Gnomad AFR exome

AF:

0.295

Gnomad AMR exome

AF:

0.158

Gnomad ASJ exome

AF:

0.350

Gnomad EAS exome

AF:

0.527

Gnomad SAS exome

AF:

0.557

Gnomad FIN exome

AF:

0.260

Gnomad NFE exome

AF:

0.299

Gnomad OTH exome

AF:

0.317

GnomAD4 exome

AF:

0.320

AC:

466114

AN:

1456788

Hom.:

79669

Cov.:

AF XY:

0.328

AC XY:

238091

AN XY:

725012

show subpopulations

Gnomad4 AFR exome

AF:

0.303

Gnomad4 AMR exome

AF:

0.164

Gnomad4 ASJ exome

AF:

0.339

Gnomad4 EAS exome

AF:

0.532

Gnomad4 SAS exome

AF:

0.555

Gnomad4 FIN exome

AF:

0.251

Gnomad4 NFE exome

AF:

0.302

Gnomad4 OTH exome

AF:

0.335

GnomAD4 genome

AF:

0.303

AC:

46003

AN:

151970

Hom.:

7447

Cov.:

AF XY:

0.305

AC XY:

22655

AN XY:

74308

show subpopulations

Gnomad4 AFR

AF:

0.296

Gnomad4 AMR

AF:

0.211

Gnomad4 ASJ

AF:

0.328

Gnomad4 EAS

AF:

0.530

Gnomad4 SAS

AF:

0.564

Gnomad4 FIN

AF:

0.263

Gnomad4 NFE

AF:

0.295

Gnomad4 OTH

AF:

0.302

Alfa

AF:

0.303

Hom.:

12726

Bravo

AF:

0.292

Asia WGS

AF:

0.485

AC:

1683

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 39% of patients studied by a panel of primary immunodeficiencies. Number of patients: 34. Only high quality variants are reported. -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.80

CADD

Benign

7.6

DANN

Benign

0.47

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