rs1343152

Variant names:

• chr1-67238649-A-C
• rs1343152
• NM_144701.3:c.1046-1530A>C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_144701.3(IL23R):​c.1046-1530A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.338 in 151,942 control chromosomes in the GnomAD database, including 9,753 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 0.34 (9753 hom., cov: 31)
• Consequence: IL23R NM_144701.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.24

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.706 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
IL23R	NM_144701.3	c.1046-1530A>C		intron_variant	Intron 8 of 10	ENST00000347310.10	NP_653302.2
IL23R	XM_011540790.4	c.1046-1530A>C		intron_variant	Intron 8 of 10		XP_011539092.1
IL23R	XM_011540791.4	c.1046-1530A>C		intron_variant	Intron 8 of 10		XP_011539093.1
IL23R	XM_047447227.1	c.1046-1530A>C		intron_variant	Intron 8 of 10		XP_047303183.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
IL23R	ENST00000347310.10	c.1046-1530A>C		intron_variant	Intron 8 of 10	1	NM_144701.3	ENSP00000321345.5

Frequencies

GnomAD3 genomes AF: 0.338 AC: 51280 AN: 151824 Hom.: 9743 Cov.: 31

Gnomad AFR AF: 0.203

Gnomad AMI AF: 0.410

Gnomad AMR AF: 0.327

Gnomad ASJ AF: 0.435

Gnomad EAS AF: 0.725

Gnomad SAS AF: 0.600

Gnomad FIN AF: 0.339

Gnomad MID AF: 0.541

Gnomad NFE AF: 0.366

Gnomad OTH AF: 0.364

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

GnomAD4 genome AF: 0.338 AC: 51314 AN: 151942 Hom.: 9753 Cov.: 31 AF XY: 0.342 AC XY: 25440 AN XY: 74280

Gnomad4 AFR AF: 0.203

Gnomad4 AMR AF: 0.327

Gnomad4 ASJ AF: 0.435

Gnomad4 EAS AF: 0.725

Gnomad4 SAS AF: 0.602

Gnomad4 FIN AF: 0.339

Gnomad4 NFE AF: 0.366

Gnomad4 OTH AF: 0.366

Alfa AF: 0.322 Hom.: 1235

Bravo AF: 0.330

Asia WGS AF: 0.589 AC: 2043 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	10
DANN	Benign	0.64

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

Publications

LitVar

Other links and lift over

dbSNP: rs1343152; hg19: chr1-67704332;