rs10889664

Variant names:

• chr1-67169792-C-T
• rs10889664
• NM_144701.3:c.367+154C>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.367+154C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.313 in 151,992 control chromosomes in the GnomAD database, including 8,043 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 0.31 (8043 hom., cov: 32)
• Consequence: IL23R NM_144701.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.755
• Publications: 12 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=-0.8).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.448 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
IL23R	NM_144701.3	c.367+154C>T		intron_variant	Intron 3 of 10	ENST00000347310.10	NP_653302.2
IL23R	XM_011540790.4	c.367+154C>T		intron_variant	Intron 3 of 10		XP_011539092.1
IL23R	XM_011540791.4	c.367+154C>T		intron_variant	Intron 3 of 10		XP_011539093.1
IL23R	XM_047447227.1	c.367+154C>T		intron_variant	Intron 3 of 10		XP_047303183.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
IL23R	ENST00000347310.10	c.367+154C>T		intron_variant	Intron 3 of 10	1	NM_144701.3	ENSP00000321345.5

Frequencies

GnomAD3 genomes AF: 0.313 AC: 47493 AN: 151874 Hom.: 8029 Cov.: 32

Gnomad AFR AF: 0.193

Gnomad AMI AF: 0.284

Gnomad AMR AF: 0.457

Gnomad ASJ AF: 0.249

Gnomad EAS AF: 0.355

Gnomad SAS AF: 0.325

Gnomad FIN AF: 0.347

Gnomad MID AF: 0.247

Gnomad NFE AF: 0.347

Gnomad OTH AF: 0.337

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

GnomAD4 genome AF: 0.313 AC: 47541 AN: 151992 Hom.: 8043 Cov.: 32 AF XY: 0.315 AC XY: 23379 AN XY: 74252

African (AFR) AF: 0.194 AC: 8027 AN: 41466

American (AMR) AF: 0.457 AC: 6982 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.249 AC: 866 AN: 3472

East Asian (EAS) AF: 0.355 AC: 1840 AN: 5184

South Asian (SAS) AF: 0.325 AC: 1561 AN: 4810

European-Finnish (FIN) AF: 0.347 AC: 3647 AN: 10510

Middle Eastern (MID) AF: 0.252 AC: 74 AN: 294

European-Non Finnish (NFE) AF: 0.347 AC: 23568 AN: 67964

Other (OTH) AF: 0.339 AC: 717 AN: 2114

Alfa AF: 0.331 Hom.: 5725

Bravo AF: 0.318

Asia WGS AF: 0.389 AC: 1350 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	11
DANN	Benign	0.74
PhyloP100		0.76
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: rs10889664; hg19: chr1-67635475;