rs11209016

Variant names:

• chr1-67197943-G-A
• rs11209016
• NM_144701.3:c.492-2794G>A

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

The NM_144701.3(IL23R):​c.492-2794G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. 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 0.0021 (0 hom., cov: 0)
• Consequence: IL23R NM_144701.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.790
• Publications: 1 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: Likely_benign. The variant received -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
IL23R	NM_144701.3	c.492-2794G>A		intron_variant	Intron 4 of 10	ENST00000347310.10	NP_653302.2
IL23R	XM_011540790.4	c.492-2794G>A		intron_variant	Intron 4 of 10		XP_011539092.1
IL23R	XM_011540791.4	c.492-2794G>A		intron_variant	Intron 4 of 10		XP_011539093.1
IL23R	XM_047447227.1	c.492-2794G>A		intron_variant	Intron 4 of 10		XP_047303183.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
IL23R	ENST00000347310.10	c.492-2794G>A		intron_variant	Intron 4 of 10	1	NM_144701.3	ENSP00000321345.5

Frequencies

GnomAD3 genomes AF: 0.00215 AC: 94 AN: 43786 Hom.: 0 Cov.: 0

Gnomad AFR AF: 0.00216

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00326

Gnomad ASJ AF: 0.000607

Gnomad EAS AF: 0.00152

Gnomad SAS AF: 0.00151

Gnomad FIN AF: 0.00484

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00182

Gnomad OTH AF: 0.00156

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

GnomAD4 genome AF: 0.00215 AC: 94 AN: 43788 Hom.: 0 Cov.: 0 AF XY: 0.00223 AC XY: 48 AN XY: 21506

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5.

African (AFR) AF: 0.00215 AC: 13 AN: 6038

American (AMR) AF: 0.00326 AC: 12 AN: 3676

Ashkenazi Jewish (ASJ) AF: 0.000607 AC: 1 AN: 1648

East Asian (EAS) AF: 0.00153 AC: 3 AN: 1964

South Asian (SAS) AF: 0.00150 AC: 3 AN: 1994

European-Finnish (FIN) AF: 0.00484 AC: 18 AN: 3720

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 128

European-Non Finnish (NFE) AF: 0.00182 AC: 43 AN: 23616

Other (OTH) AF: 0.00155 AC: 1 AN: 646

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5. (p-value = 0.000000), which strongly suggests a high chance of mosaicism in these individuals.

Alfa AF: 0.00 Hom.: 0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.12
DANN	Benign	0.11
PhyloP100		-0.79
Mutation Taster		=100/0	polymorphism

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: rs11209016; hg19: chr1-67663626;