rs10889675

Variant names:

• chr1-67256533-C-A
• rs10889675
• NM_144701.3:c.1239+606C>A

Your query was ambiguous. Multiple possible variants found:

• chr1-67256533-C-A
• chr1-67256533-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+606C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.117 in 152,152 control chromosomes in the GnomAD database, including 1,574 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 0.12 (1574 hom., cov: 32)
• Consequence: IL23R NM_144701.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.475
• Publications: 20 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=-0.86).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.258 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
IL23R	NM_144701.3	c.1239+606C>A		intron_variant	Intron 10 of 10	ENST00000347310.10	NP_653302.2
IL23R	XM_011540790.4	c.1239+606C>A		intron_variant	Intron 10 of 10		XP_011539092.1
IL23R	XM_011540791.4	c.1239+606C>A		intron_variant	Intron 10 of 10		XP_011539093.1
IL23R	XM_047447227.1	c.1239+606C>A		intron_variant	Intron 10 of 10		XP_047303183.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
IL23R	ENST00000347310.10	c.1239+606C>A		intron_variant	Intron 10 of 10	1	NM_144701.3	ENSP00000321345.5

Frequencies

GnomAD3 genomes AF: 0.117 AC: 17844 AN: 152034 Hom.: 1567 Cov.: 32

Gnomad AFR AF: 0.0268

Gnomad AMI AF: 0.0329

Gnomad AMR AF: 0.264

Gnomad ASJ AF: 0.130

Gnomad EAS AF: 0.206

Gnomad SAS AF: 0.131

Gnomad FIN AF: 0.210

Gnomad MID AF: 0.0601

Gnomad NFE AF: 0.118

Gnomad OTH AF: 0.122

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

GnomAD4 genome AF: 0.117 AC: 17856 AN: 152152 Hom.: 1574 Cov.: 32 AF XY: 0.125 AC XY: 9296 AN XY: 74384

African (AFR) AF: 0.0267 AC: 1110 AN: 41538

American (AMR) AF: 0.265 AC: 4045 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.130 AC: 450 AN: 3472

East Asian (EAS) AF: 0.207 AC: 1068 AN: 5170

South Asian (SAS) AF: 0.129 AC: 624 AN: 4820

European-Finnish (FIN) AF: 0.210 AC: 2220 AN: 10590

Middle Eastern (MID) AF: 0.0612 AC: 18 AN: 294

European-Non Finnish (NFE) AF: 0.118 AC: 8032 AN: 67972

Other (OTH) AF: 0.123 AC: 259 AN: 2112

Alfa AF: 0.115 Hom.: 2551

Bravo AF: 0.119

Asia WGS AF: 0.170 AC: 591 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	1.3
DANN	Benign	0.56
PhyloP100		-0.47
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: rs10889675; hg19: chr1-67722216;