XM_047447227.1:c.1239+4494T>C

Variant names:

• chr1-67260421-T-C
• rs9988642
• XM_047447227.1:c.1239+4494T>C

Variant summary

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

The XM_047447227.1(IL23R):​c.1239+4494T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.127 in 152,112 control chromosomes in the GnomAD database, including 1,963 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 0.13 (1963 hom., cov: 31)
• Consequence: IL23R XM_047447227.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.424
• Publications: 39 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]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.28 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.127 AC: 19364 AN: 151994 Hom.: 1960 Cov.: 31

Gnomad AFR AF: 0.284

Gnomad AMI AF: 0.132

Gnomad AMR AF: 0.0880

Gnomad ASJ AF: 0.0957

Gnomad EAS AF: 0.000577

Gnomad SAS AF: 0.0313

Gnomad FIN AF: 0.0603

Gnomad MID AF: 0.123

Gnomad NFE AF: 0.0700

Gnomad OTH AF: 0.109

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

GnomAD4 genome AF: 0.127 AC: 19388 AN: 152112 Hom.: 1963 Cov.: 31 AF XY: 0.124 AC XY: 9218 AN XY: 74362

African (AFR) AF: 0.284 AC: 11781 AN: 41460

American (AMR) AF: 0.0878 AC: 1341 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.0957 AC: 332 AN: 3468

East Asian (EAS) AF: 0.000578 AC: 3 AN: 5188

South Asian (SAS) AF: 0.0311 AC: 150 AN: 4820

European-Finnish (FIN) AF: 0.0603 AC: 638 AN: 10586

Middle Eastern (MID) AF: 0.119 AC: 35 AN: 294

European-Non Finnish (NFE) AF: 0.0700 AC: 4759 AN: 68004

Other (OTH) AF: 0.108 AC: 229 AN: 2116

Alfa AF: 0.0942 Hom.: 2078

Bravo AF: 0.137

Asia WGS AF: 0.0300 AC: 103 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	5.1
DANN	Benign	0.51
PhyloP100		-0.42

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs9988642; hg19: chr1-67726104;