rs10489628

Positions:

• chr1-67238424-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_144701.3(IL23R):​c.1045+1622G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.426 in 151,558 control chromosomes in the GnomAD database, including 14,319 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 0.43 (14319 hom., cov: 30)
• Consequence: IL23R NM_144701.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.17

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.521 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
IL23R	NM_144701.3	c.1045+1622G>A		intron_variant		ENST00000347310.10	NP_653302.2
IL23R	XM_011540790.4	c.1045+1622G>A		intron_variant			XP_011539092.1
IL23R	XM_011540791.4	c.1045+1622G>A		intron_variant			XP_011539093.1
IL23R	XM_047447227.1	c.1045+1622G>A		intron_variant			XP_047303183.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
IL23R	ENST00000347310.10	c.1045+1622G>A		intron_variant		1	NM_144701.3	ENSP00000321345.5

Frequencies

GnomAD3 genomes AF: 0.426 AC: 64513 AN: 151448 Hom.: 14306 Cov.: 30

Gnomad AFR AF: 0.527

Gnomad AMI AF: 0.335

Gnomad AMR AF: 0.478

Gnomad ASJ AF: 0.333

Gnomad EAS AF: 0.260

Gnomad SAS AF: 0.265

Gnomad FIN AF: 0.369

Gnomad MID AF: 0.278

Gnomad NFE AF: 0.393

Gnomad OTH AF: 0.397

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

GnomAD4 genome AF: 0.426 AC: 64572 AN: 151558 Hom.: 14319 Cov.: 30 AF XY: 0.422 AC XY: 31244 AN XY: 74024

Gnomad4 AFR AF: 0.527

Gnomad4 AMR AF: 0.479

Gnomad4 ASJ AF: 0.333

Gnomad4 EAS AF: 0.260

Gnomad4 SAS AF: 0.263

Gnomad4 FIN AF: 0.369

Gnomad4 NFE AF: 0.393

Gnomad4 OTH AF: 0.397

Alfa AF: 0.402 Hom.: 7495

Bravo AF: 0.440

Asia WGS AF: 0.335 AC: 1169 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	0.56
DANN	Benign	0.59

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

Other links and lift over

dbSNP: rs10489628; hg19: chr1-67704107;