1-67182611-C-T

Variant names:

• chr1-67182611-C-T
• rs11465788
• NM_144701.3:c.368-225C>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.368-225C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.476 in 151,938 control chromosomes in the GnomAD database, including 17,870 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 0.48 (17870 hom., cov: 31)
• Consequence: IL23R NM_144701.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.145
• Publications: 9 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 = 0.623 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
IL23R	NM_144701.3	c.368-225C>T		intron_variant	Intron 3 of 10	ENST00000347310.10	NP_653302.2
IL23R	XM_011540790.4	c.368-225C>T		intron_variant	Intron 3 of 10		XP_011539092.1
IL23R	XM_011540791.4	c.368-225C>T		intron_variant	Intron 3 of 10		XP_011539093.1
IL23R	XM_047447227.1	c.368-225C>T		intron_variant	Intron 3 of 10		XP_047303183.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
IL23R	ENST00000347310.10	c.368-225C>T		intron_variant	Intron 3 of 10	1	NM_144701.3	ENSP00000321345.5

Frequencies

GnomAD3 genomes AF: 0.476 AC: 72273 AN: 151820 Hom.: 17869 Cov.: 31

Gnomad AFR AF: 0.357

Gnomad AMI AF: 0.647

Gnomad AMR AF: 0.398

Gnomad ASJ AF: 0.610

Gnomad EAS AF: 0.642

Gnomad SAS AF: 0.627

Gnomad FIN AF: 0.512

Gnomad MID AF: 0.541

Gnomad NFE AF: 0.529

Gnomad OTH AF: 0.448

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

GnomAD4 genome AF: 0.476 AC: 72278 AN: 151938 Hom.: 17870 Cov.: 31 AF XY: 0.476 AC XY: 35387 AN XY: 74272

African (AFR) AF: 0.356 AC: 14749 AN: 41422

American (AMR) AF: 0.398 AC: 6078 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.610 AC: 2116 AN: 3470

East Asian (EAS) AF: 0.642 AC: 3299 AN: 5142

South Asian (SAS) AF: 0.627 AC: 3021 AN: 4820

European-Finnish (FIN) AF: 0.512 AC: 5404 AN: 10562

Middle Eastern (MID) AF: 0.545 AC: 159 AN: 292

European-Non Finnish (NFE) AF: 0.529 AC: 35919 AN: 67944

Other (OTH) AF: 0.447 AC: 943 AN: 2110

Alfa AF: 0.494 Hom.: 2331

Bravo AF: 0.460

Asia WGS AF: 0.555 AC: 1931 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	3.6
DANN	Benign	0.46
PhyloP100		0.14
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: rs11465788; hg19: chr1-67648294;