rs10889676

Variant names:

• chr1-67256884-C-A
• rs10889676
• NM_144701.3:c.1239+957C>A

Your query was ambiguous. Multiple possible variants found:

• chr1-67256884-C-A
• chr1-67256884-C-G
• chr1-67256884-C-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.1239+957C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.285 in 152,084 control chromosomes in the GnomAD database, including 7,329 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 0.28 (7329 hom., cov: 32)
• Consequence: IL23R NM_144701.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.02
• Publications: 17 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=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.706 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.1239+957C>A		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.1239+957C>A		intron	N/A	ENSP00000321345.5	Q5VWK5-1
	IL23R	ENST00000425614.3	TSL:1	c.474+957C>A		intron	N/A	ENSP00000387640.2	Q5VWK5-6
	IL23R	ENST00000473881.2	TSL:1	n.*65+957C>A		intron	N/A	ENSP00000486667.1	A0A0D9SFJ7

Frequencies

GnomAD3 genomes AF: 0.285 AC: 43251 AN: 151966 Hom.: 7321 Cov.: 32

Gnomad AFR AF: 0.159

Gnomad AMI AF: 0.310

Gnomad AMR AF: 0.267

Gnomad ASJ AF: 0.344

Gnomad EAS AF: 0.725

Gnomad SAS AF: 0.588

Gnomad FIN AF: 0.293

Gnomad MID AF: 0.443

Gnomad NFE AF: 0.304

Gnomad OTH AF: 0.309

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

GnomAD4 genome AF: 0.285 AC: 43282 AN: 152084 Hom.: 7329 Cov.: 32 AF XY: 0.291 AC XY: 21598 AN XY: 74340

African (AFR) AF: 0.159 AC: 6610 AN: 41504

American (AMR) AF: 0.267 AC: 4081 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.344 AC: 1194 AN: 3468

East Asian (EAS) AF: 0.725 AC: 3739 AN: 5154

South Asian (SAS) AF: 0.589 AC: 2837 AN: 4816

European-Finnish (FIN) AF: 0.293 AC: 3094 AN: 10568

Middle Eastern (MID) AF: 0.442 AC: 129 AN: 292

European-Non Finnish (NFE) AF: 0.304 AC: 20660 AN: 67982

Other (OTH) AF: 0.311 AC: 656 AN: 2108

Alfa AF: 0.301 Hom.: 29082

Bravo AF: 0.274

Asia WGS AF: 0.578 AC: 2006 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.6
DANN	Benign	0.24
PhyloP100		-1.0
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: rs10889676; hg19: chr1-67722567;