NM_144701.3:c.1149-2391G>A

Variant names:

• chr1-67253446-G-A
• rs1343151
• NM_144701.3:c.1149-2391G>A

Variant summary

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

The NM_144701.3(IL23R):​c.1149-2391G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.404 in 152,018 control chromosomes in the GnomAD database, including 15,100 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 0.40 (15100 hom., cov: 32)
• Consequence: IL23R NM_144701.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0970
• Publications: 104 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=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.674 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	IL23R	NM_144701.3	MANE Select	c.1149-2391G>A		intron	N/A	NP_653302.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	IL23R	ENST00000347310.10	TSL:1 MANE Select	c.1149-2391G>A		intron	N/A	ENSP00000321345.5
	IL23R	ENST00000425614.3	TSL:1	c.384-2391G>A		intron	N/A	ENSP00000387640.2
	IL23R	ENST00000473881.2	TSL:1	n.191-2391G>A		intron	N/A	ENSP00000486667.1

Frequencies

GnomAD3 genomes AF: 0.404 AC: 61345 AN: 151900 Hom.: 15079 Cov.: 32

Gnomad AFR AF: 0.681

Gnomad AMI AF: 0.404

Gnomad AMR AF: 0.291

Gnomad ASJ AF: 0.299

Gnomad EAS AF: 0.0550

Gnomad SAS AF: 0.150

Gnomad FIN AF: 0.211

Gnomad MID AF: 0.316

Gnomad NFE AF: 0.342

Gnomad OTH AF: 0.364

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

GnomAD4 genome AF: 0.404 AC: 61408 AN: 152018 Hom.: 15100 Cov.: 32 AF XY: 0.390 AC XY: 28946 AN XY: 74310

African (AFR) AF: 0.680 AC: 28212 AN: 41468

American (AMR) AF: 0.290 AC: 4431 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.299 AC: 1037 AN: 3470

East Asian (EAS) AF: 0.0547 AC: 283 AN: 5174

South Asian (SAS) AF: 0.150 AC: 721 AN: 4816

European-Finnish (FIN) AF: 0.211 AC: 2230 AN: 10550

Middle Eastern (MID) AF: 0.320 AC: 94 AN: 294

European-Non Finnish (NFE) AF: 0.342 AC: 23269 AN: 67952

Other (OTH) AF: 0.362 AC: 763 AN: 2108

Alfa AF: 0.364 Hom.: 39712

Bravo AF: 0.423

Asia WGS AF: 0.179 AC: 625 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	3.9
DANN	Benign	0.83
PhyloP100		-0.097
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: rs1343151; hg19: chr1-67719129;