rs11465770

chr1-67168280-C-T

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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/exons	MANE	UniProt
IL23R	NM_144701.3	c.70+90C>T		intron_variant		ENST00000347310.10
IL23R	XM_011540790.4	c.70+90C>T		intron_variant
IL23R	XM_011540791.4	c.70+90C>T		intron_variant
IL23R	XM_047447227.1	c.70+90C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
IL23R	ENST00000347310.10	c.70+90C>T		intron_variant		1	NM_144701.3	P1

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

Gnomad4 AFR exome AF: 0.0138

Gnomad4 AMR exome AF: 0.0367

Gnomad4 ASJ exome AF: 0.0979

Gnomad4 EAS exome AF: 0.000436

Gnomad4 SAS exome AF: 0.0791

Gnomad4 FIN exome AF: 0.112

Gnomad4 NFE exome AF: 0.103

Gnomad4 OTH exome AF: 0.0818

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

Gnomad4 AFR AF: 0.0168

Gnomad4 AMR AF: 0.0520

Gnomad4 ASJ AF: 0.106

Gnomad4 EAS AF: 0.000386

Gnomad4 SAS AF: 0.0716

Gnomad4 FIN AF: 0.109

Gnomad4 NFE AF: 0.102

Gnomad4 OTH AF: 0.0772

Alfa AF: 0.0894 Hom.: 429

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

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: rs11465770; hg19: chr1-67633963;