rs790632

Variant names:

• chr1-67213239-C-A
• rs790632
• NM_144701.3:c.798+6184C>A

Your query was ambiguous. Multiple possible variants found:

• chr1-67213239-C-A
• chr1-67213239-C-G
• chr1-67213239-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.798+6184C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.803 in 152,090 control chromosomes in the GnomAD database, including 49,665 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 0.80 (49665 hom., cov: 32)
• Consequence: IL23R NM_144701.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.09
• Publications: 6 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=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.948 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_144701.3. 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
	IL23R	NM_144701.3	MANE Select	c.798+6184C>A		intron	N/A	NP_653302.2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	IL23R	ENST00000347310.10	TSL:1 MANE Select	c.798+6184C>A		intron	N/A	ENSP00000321345.5	Q5VWK5-1
	IL23R	ENST00000425614.3	TSL:1	c.33+5541C>A		intron	N/A	ENSP00000387640.2	Q5VWK5-6
	IL23R	ENST00000473881.2	TSL:1	n.33+5541C>A		intron	N/A	ENSP00000486667.1	A0A0D9SFJ7

Frequencies

GnomAD3 genomes AF: 0.803 AC: 122012 AN: 151974 Hom.: 49605 Cov.: 32

Gnomad AFR AF: 0.921

Gnomad AMI AF: 0.754

Gnomad AMR AF: 0.796

Gnomad ASJ AF: 0.706

Gnomad EAS AF: 0.970

Gnomad SAS AF: 0.863

Gnomad FIN AF: 0.698

Gnomad MID AF: 0.782

Gnomad NFE AF: 0.738

Gnomad OTH AF: 0.769

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

GnomAD4 genome AF: 0.803 AC: 122128 AN: 152090 Hom.: 49665 Cov.: 32 AF XY: 0.802 AC XY: 59633 AN XY: 74330

African (AFR) AF: 0.921 AC: 38232 AN: 41502

American (AMR) AF: 0.796 AC: 12160 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.706 AC: 2444 AN: 3464

East Asian (EAS) AF: 0.970 AC: 5029 AN: 5184

South Asian (SAS) AF: 0.862 AC: 4157 AN: 4822

European-Finnish (FIN) AF: 0.698 AC: 7355 AN: 10530

Middle Eastern (MID) AF: 0.786 AC: 231 AN: 294

European-Non Finnish (NFE) AF: 0.738 AC: 50208 AN: 68000

Other (OTH) AF: 0.771 AC: 1624 AN: 2106

Alfa AF: 0.737 Hom.: 7874

Bravo AF: 0.814

Asia WGS AF: 0.914 AC: 3175 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.29
DANN	Benign	0.40
PhyloP100		-1.1
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: rs790632; hg19: chr1-67678922;