rs11465770

Variant names:

• chr1-67168280-C-T
• rs11465770
• NM_144701.3:c.70+90C>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.70+90C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0864 in 982,694 control chromosomes in the GnomAD database, including 4,272 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 0.069 (485 hom., cov: 32)
  • Exomes 𝑓: 0.090 (3787 hom.)
• Consequence: IL23R NM_144701.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.210
• Publications: 11 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]

C1orf141 (HGNC:32044): (chromosome 1 open reading frame 141)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.1 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
IL23R	NM_144701.3	c.70+90C>T		intron_variant	Intron 2 of 10	ENST00000347310.10	NP_653302.2
IL23R	XM_011540790.4	c.70+90C>T		intron_variant	Intron 2 of 10		XP_011539092.1
IL23R	XM_011540791.4	c.70+90C>T		intron_variant	Intron 2 of 10		XP_011539093.1
IL23R	XM_047447227.1	c.70+90C>T		intron_variant	Intron 2 of 10		XP_047303183.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
IL23R	ENST00000347310.10	c.70+90C>T		intron_variant	Intron 2 of 10	1	NM_144701.3	ENSP00000321345.5

Frequencies

GnomAD3 genomes AF: 0.0694 AC: 10546 AN: 151974 Hom.: 485 Cov.: 32

Gnomad AFR AF: 0.0169

Gnomad AMI AF: 0.0936

Gnomad AMR AF: 0.0521

Gnomad ASJ AF: 0.106

Gnomad EAS AF: 0.000385

Gnomad SAS AF: 0.0715

Gnomad FIN AF: 0.109

Gnomad MID AF: 0.0411

Gnomad NFE AF: 0.102

Gnomad OTH AF: 0.0780

GnomAD4 exome AF: 0.0895 AC: 74353 AN: 830602 Hom.: 3787 AF XY: 0.0901 AC XY: 39489 AN XY: 438334

African (AFR) AF: 0.0138 AC: 293 AN: 21230

American (AMR) AF: 0.0367 AC: 1598 AN: 43506

Ashkenazi Jewish (ASJ) AF: 0.0979 AC: 2162 AN: 22086

East Asian (EAS) AF: 0.000436 AC: 16 AN: 36672

South Asian (SAS) AF: 0.0791 AC: 5726 AN: 72394

European-Finnish (FIN) AF: 0.112 AC: 5603 AN: 49920

Middle Eastern (MID) AF: 0.0627 AC: 274 AN: 4370

European-Non Finnish (NFE) AF: 0.103 AC: 55441 AN: 540792

Other (OTH) AF: 0.0818 AC: 3240 AN: 39632

GnomAD4 genome AF: 0.0693 AC: 10546 AN: 152092 Hom.: 485 Cov.: 32 AF XY: 0.0692 AC XY: 5141 AN XY: 74344

African (AFR) AF: 0.0168 AC: 698 AN: 41498

American (AMR) AF: 0.0520 AC: 794 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.106 AC: 366 AN: 3468

East Asian (EAS) AF: 0.000386 AC: 2 AN: 5188

South Asian (SAS) AF: 0.0716 AC: 345 AN: 4820

European-Finnish (FIN) AF: 0.109 AC: 1145 AN: 10548

Middle Eastern (MID) AF: 0.0442 AC: 13 AN: 294

European-Non Finnish (NFE) AF: 0.102 AC: 6935 AN: 67982

Other (OTH) AF: 0.0772 AC: 163 AN: 2112

Alfa AF: 0.0908 Hom.: 723

Bravo AF: 0.0614

Asia WGS AF: 0.0320 AC: 111 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	5.6
DANN	Benign	0.37
PhyloP100		0.21
Mutation Taster		=100/0	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: rs11465770; hg19: chr1-67633963;