rs2863212

Variant names:

• chr1-67219433-C-T
• rs2863212
• NM_144701.3:c.799-141C>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.799-141C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.889 in 732,406 control chromosomes in the GnomAD database, including 290,068 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 0.86 (56972 hom., cov: 33)
  • Exomes 𝑓: 0.90 (233096 hom.)
• Consequence: IL23R NM_144701.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0300
• Publications: 16 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=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.964 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_144701.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	IL23R	NM_144701.3	MANE Select	c.799-141C>T		intron	N/A	NP_653302.2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	IL23R	ENST00000347310.10	TSL:1 MANE Select	c.799-141C>T		intron	N/A	ENSP00000321345.5	Q5VWK5-1
	IL23R	ENST00000425614.3	TSL:1	c.34-141C>T		intron	N/A	ENSP00000387640.2	Q5VWK5-6
	IL23R	ENST00000473881.2	TSL:1	n.34-141C>T		intron	N/A	ENSP00000486667.1	A0A0D9SFJ7

Frequencies

GnomAD3 genomes AF: 0.863 AC: 131281 AN: 152124 Hom.: 56938 Cov.: 33

Gnomad AFR AF: 0.783

Gnomad AMI AF: 0.935

Gnomad AMR AF: 0.880

Gnomad ASJ AF: 0.920

Gnomad EAS AF: 0.986

Gnomad SAS AF: 0.970

Gnomad FIN AF: 0.854

Gnomad MID AF: 0.873

Gnomad NFE AF: 0.888

Gnomad OTH AF: 0.862

GnomAD4 exome AF: 0.895 AC: 519403 AN: 580164 Hom.: 233096 AF XY: 0.899 AC XY: 278833 AN XY: 310208

African (AFR) AF: 0.777 AC: 11876 AN: 15284

American (AMR) AF: 0.907 AC: 25160 AN: 27748

Ashkenazi Jewish (ASJ) AF: 0.918 AC: 16386 AN: 17848

East Asian (EAS) AF: 0.988 AC: 31839 AN: 32232

South Asian (SAS) AF: 0.966 AC: 53871 AN: 55742

European-Finnish (FIN) AF: 0.837 AC: 27233 AN: 32536

Middle Eastern (MID) AF: 0.882 AC: 2117 AN: 2400

European-Non Finnish (NFE) AF: 0.885 AC: 323320 AN: 365392

Other (OTH) AF: 0.891 AC: 27601 AN: 30982

GnomAD4 genome AF: 0.863 AC: 131371 AN: 152242 Hom.: 56972 Cov.: 33 AF XY: 0.864 AC XY: 64295 AN XY: 74440

African (AFR) AF: 0.783 AC: 32510 AN: 41510

American (AMR) AF: 0.880 AC: 13461 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.920 AC: 3191 AN: 3468

East Asian (EAS) AF: 0.986 AC: 5121 AN: 5192

South Asian (SAS) AF: 0.970 AC: 4685 AN: 4830

European-Finnish (FIN) AF: 0.854 AC: 9051 AN: 10602

Middle Eastern (MID) AF: 0.881 AC: 259 AN: 294

European-Non Finnish (NFE) AF: 0.888 AC: 60418 AN: 68026

Other (OTH) AF: 0.863 AC: 1824 AN: 2114

Alfa AF: 0.886 Hom.: 92570

Bravo AF: 0.860

Asia WGS AF: 0.966 AC: 3359 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	2.8
DANN	Benign	0.77
PhyloP100		-0.030
PromoterAI		0.043	Neutral
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: rs2863212; hg19: chr1-67685116;