rs11465803

Variant names:

• chr1-67236458-C-T
• rs11465803
• NM_144701.3:c.956-255C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_144701.3(IL23R):​c.956-255C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0885 in 152,260 control chromosomes in the GnomAD database, including 711 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 0.089 (711 hom., cov: 33)
• Consequence: IL23R NM_144701.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.159
• Publications: 6 publications found

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

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.109 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
IL23R	NM_144701.3	c.956-255C>T		intron_variant	Intron 7 of 10	ENST00000347310.10	NP_653302.2
IL23R	XM_011540790.4	c.956-255C>T		intron_variant	Intron 7 of 10		XP_011539092.1
IL23R	XM_011540791.4	c.956-255C>T		intron_variant	Intron 7 of 10		XP_011539093.1
IL23R	XM_047447227.1	c.956-255C>T		intron_variant	Intron 7 of 10		XP_047303183.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
IL23R	ENST00000347310.10	c.956-255C>T		intron_variant	Intron 7 of 10	1	NM_144701.3	ENSP00000321345.5

Frequencies

GnomAD3 genomes AF: 0.0886 AC: 13481 AN: 152142 Hom.: 711 Cov.: 33

Gnomad AFR AF: 0.0533

Gnomad AMI AF: 0.174

Gnomad AMR AF: 0.0651

Gnomad ASJ AF: 0.135

Gnomad EAS AF: 0.000192

Gnomad SAS AF: 0.0704

Gnomad FIN AF: 0.149

Gnomad MID AF: 0.0380

Gnomad NFE AF: 0.111

Gnomad OTH AF: 0.0865

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

GnomAD4 genome AF: 0.0885 AC: 13481 AN: 152260 Hom.: 711 Cov.: 33 AF XY: 0.0897 AC XY: 6675 AN XY: 74442

African (AFR) AF: 0.0532 AC: 2212 AN: 41550

American (AMR) AF: 0.0650 AC: 994 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.135 AC: 467 AN: 3470

East Asian (EAS) AF: 0.000193 AC: 1 AN: 5192

South Asian (SAS) AF: 0.0702 AC: 339 AN: 4828

European-Finnish (FIN) AF: 0.149 AC: 1573 AN: 10586

Middle Eastern (MID) AF: 0.0408 AC: 12 AN: 294

European-Non Finnish (NFE) AF: 0.111 AC: 7543 AN: 68014

Other (OTH) AF: 0.0856 AC: 181 AN: 2114

Alfa AF: 0.0959 Hom.: 145

Bravo AF: 0.0804

Asia WGS AF: 0.0350 AC: 125 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	11
DANN	Benign	0.71
PhyloP100		0.16
Mutation Taster		=98/2	polymorphism (auto)

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

Other links and lift over

dbSNP: rs11465803; hg19: chr1-67702141;