rs10889676

Positions:

• chr1-67256884-C-A
• chr1-67256884-C-G
• chr1-67256884-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.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

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

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
IL23R	NM_144701.3	c.1239+957C>A		intron_variant		ENST00000347310.10	NP_653302.2
IL23R	XM_011540790.4	c.1239+957C>A		intron_variant			XP_011539092.1
IL23R	XM_011540791.4	c.1239+957C>A		intron_variant			XP_011539093.1
IL23R	XM_047447227.1	c.1239+957C>A		intron_variant			XP_047303183.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
IL23R	ENST00000347310.10	c.1239+957C>A		intron_variant		1	NM_144701.3	ENSP00000321345	P1

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

Gnomad4 AFR AF: 0.159

Gnomad4 AMR AF: 0.267

Gnomad4 ASJ AF: 0.344

Gnomad4 EAS AF: 0.725

Gnomad4 SAS AF: 0.589

Gnomad4 FIN AF: 0.293

Gnomad4 NFE AF: 0.304

Gnomad4 OTH AF: 0.311

Alfa AF: 0.310 Hom.: 13502

Bravo AF: 0.274

Asia WGS AF: 0.578 AC: 2006 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.6
DANN	Benign	0.24

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: rs10889676; hg19: chr1-67722567;