rs10489629

chr1-67222666-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_144701.3(IL23R):c.955+2936T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.476 in 152,028 control chromosomes in the GnomAD database, including 17,751 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 0.48 (17751 hom., cov: 31)
• Consequence: IL23R NM_144701.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.28

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.552 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
IL23R	NM_144701.3	c.955+2936T>C		intron_variant		ENST00000347310.10
IL23R	XM_011540790.4	c.955+2936T>C		intron_variant
IL23R	XM_011540791.4	c.955+2936T>C		intron_variant
IL23R	XM_047447227.1	c.955+2936T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
IL23R	ENST00000347310.10	c.955+2936T>C		intron_variant		1	NM_144701.3	P1

Frequencies

GnomAD3 genomes AF: 0.476 AC: 72296 AN: 151910 Hom.: 17738 Cov.: 31

Gnomad AFR AF: 0.558

Gnomad AMI AF: 0.435

Gnomad AMR AF: 0.539

Gnomad ASJ AF: 0.428

Gnomad EAS AF: 0.264

Gnomad SAS AF: 0.278

Gnomad FIN AF: 0.413

Gnomad MID AF: 0.380

Gnomad NFE AF: 0.456

Gnomad OTH AF: 0.455

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

GnomAD4 genome AF: 0.476 AC: 72357 AN: 152028 Hom.: 17751 Cov.: 31 AF XY: 0.470 AC XY: 34942 AN XY: 74304

Gnomad4 AFR AF: 0.558

Gnomad4 AMR AF: 0.539

Gnomad4 ASJ AF: 0.428

Gnomad4 EAS AF: 0.264

Gnomad4 SAS AF: 0.277

Gnomad4 FIN AF: 0.413

Gnomad4 NFE AF: 0.456

Gnomad4 OTH AF: 0.455

Alfa AF: 0.458 Hom.: 33965

Bravo AF: 0.493

Asia WGS AF: 0.344 AC: 1198 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	0.60
Dann	Benign	0.51

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: rs10489629; hg19: chr1-67688349;