rs11465754

Variant names:

• chr1-67165748-A-G
• rs11465754
• ENST00000637002.1:n.-29-2344A>G

Your query was ambiguous. Multiple possible variants found:

• chr1-67165748-A-G
• chr1-67165748-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.-29-2344A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.386 in 151,908 control chromosomes in the GnomAD database, including 11,701 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 (11701 hom., cov: 33)
• Consequence: IL23R ENST00000697222.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.05
• 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=-0.93).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.472 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.-29-2344A>G		intron	N/A	ENSP00000490340.2
	C1orf141	ENST00000371007.6	TSL:5	c.-103-34521T>C		intron	N/A	ENSP00000360046.1
	C1orf141	ENST00000448166.6	TSL:5	c.-103-34521T>C		intron	N/A	ENSP00000415519.2

Frequencies

GnomAD3 genomes AF: 0.386 AC: 58608 AN: 151786 Hom.: 11667 Cov.: 33

Gnomad AFR AF: 0.462

Gnomad AMI AF: 0.280

Gnomad AMR AF: 0.481

Gnomad ASJ AF: 0.249

Gnomad EAS AF: 0.382

Gnomad SAS AF: 0.322

Gnomad FIN AF: 0.338

Gnomad MID AF: 0.242

Gnomad NFE AF: 0.340

Gnomad OTH AF: 0.391

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

GnomAD4 genome AF: 0.386 AC: 58699 AN: 151908 Hom.: 11701 Cov.: 33 AF XY: 0.387 AC XY: 28704 AN XY: 74250

African (AFR) AF: 0.462 AC: 19159 AN: 41456

American (AMR) AF: 0.481 AC: 7333 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.249 AC: 863 AN: 3466

East Asian (EAS) AF: 0.382 AC: 1976 AN: 5170

South Asian (SAS) AF: 0.321 AC: 1545 AN: 4820

European-Finnish (FIN) AF: 0.338 AC: 3563 AN: 10526

Middle Eastern (MID) AF: 0.248 AC: 73 AN: 294

European-Non Finnish (NFE) AF: 0.340 AC: 23103 AN: 67918

Other (OTH) AF: 0.393 AC: 831 AN: 2112

Alfa AF: 0.383 Hom.: 4742

Bravo AF: 0.403

Asia WGS AF: 0.414 AC: 1438 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.32
DANN	Benign	0.30
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: rs11465754; hg19: chr1-67631431;