rs10789226

Variant names:

• chr1-67158045-A-G
• rs10789226
• ENST00000637002.1:n.-29-10047A>G

Your query was ambiguous. Multiple possible variants found:

• chr1-67158045-A-G
• chr1-67158045-A-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000697222.1(IL23R):​c.-29-10047A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.392 in 151,724 control chromosomes in the GnomAD database, including 12,128 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 0.39 (12128 hom., cov: 30)
• Consequence: IL23R ENST00000697222.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.623
• Publications: 5 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=-1.0).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.477 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000697222.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	IL23R	ENST00000637002.1	TSL:1	n.-29-10047A>G		intron	N/A	ENSP00000490340.2	A0A1B0GV19
	C1orf141	ENST00000371007.6	TSL:5	c.-103-26818T>C		intron	N/A	ENSP00000360046.1	Q5JVX7-1
	C1orf141	ENST00000448166.6	TSL:5	c.-103-26818T>C		intron	N/A	ENSP00000415519.2	Q5JVX6

Frequencies

GnomAD3 genomes AF: 0.392 AC: 59447 AN: 151606 Hom.: 12095 Cov.: 30

Gnomad AFR AF: 0.482

Gnomad AMI AF: 0.284

Gnomad AMR AF: 0.484

Gnomad ASJ AF: 0.252

Gnomad EAS AF: 0.384

Gnomad SAS AF: 0.322

Gnomad FIN AF: 0.339

Gnomad MID AF: 0.239

Gnomad NFE AF: 0.340

Gnomad OTH AF: 0.395

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

GnomAD4 genome AF: 0.392 AC: 59537 AN: 151724 Hom.: 12128 Cov.: 30 AF XY: 0.392 AC XY: 29071 AN XY: 74118

African (AFR) AF: 0.483 AC: 19953 AN: 41346

American (AMR) AF: 0.484 AC: 7376 AN: 15240

Ashkenazi Jewish (ASJ) AF: 0.252 AC: 873 AN: 3468

East Asian (EAS) AF: 0.384 AC: 1972 AN: 5140

South Asian (SAS) AF: 0.321 AC: 1542 AN: 4810

European-Finnish (FIN) AF: 0.339 AC: 3562 AN: 10504

Middle Eastern (MID) AF: 0.240 AC: 70 AN: 292

European-Non Finnish (NFE) AF: 0.340 AC: 23093 AN: 67908

Other (OTH) AF: 0.398 AC: 838 AN: 2108

Alfa AF: 0.358 Hom.: 1218

Bravo AF: 0.409

Asia WGS AF: 0.415 AC: 1443 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.29
DANN	Benign	0.62
PhyloP100		-0.62
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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs10789226;

hg19: chr1-67623728;