1-67211239-C-T

Variant names:

• chr1-67211239-C-T
• rs790631
• NM_144701.3:c.798+4184C>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+4184C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.77 in 152,148 control chromosomes in the GnomAD database, including 45,420 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 0.77 (45420 hom., cov: 33)
• Consequence: IL23R NM_144701.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.274
• Publications: 13 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 = 0.947 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
IL23R	NM_144701.3	c.798+4184C>T		intron_variant	Intron 6 of 10	ENST00000347310.10	NP_653302.2
IL23R	XM_011540790.4	c.798+4184C>T		intron_variant	Intron 6 of 10		XP_011539092.1
IL23R	XM_011540791.4	c.798+4184C>T		intron_variant	Intron 6 of 10		XP_011539093.1
IL23R	XM_047447227.1	c.798+4184C>T		intron_variant	Intron 6 of 10		XP_047303183.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
IL23R	ENST00000347310.10	c.798+4184C>T		intron_variant	Intron 6 of 10	1	NM_144701.3	ENSP00000321345.5

Frequencies

GnomAD3 genomes AF: 0.770 AC: 117096 AN: 152030 Hom.: 45378 Cov.: 33

Gnomad AFR AF: 0.810

Gnomad AMI AF: 0.754

Gnomad AMR AF: 0.783

Gnomad ASJ AF: 0.677

Gnomad EAS AF: 0.970

Gnomad SAS AF: 0.863

Gnomad FIN AF: 0.698

Gnomad MID AF: 0.737

Gnomad NFE AF: 0.738

Gnomad OTH AF: 0.743

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

GnomAD4 genome AF: 0.770 AC: 117192 AN: 152148 Hom.: 45420 Cov.: 33 AF XY: 0.771 AC XY: 57330 AN XY: 74370

African (AFR) AF: 0.810 AC: 33622 AN: 41510

American (AMR) AF: 0.784 AC: 11975 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.677 AC: 2350 AN: 3472

East Asian (EAS) AF: 0.970 AC: 5031 AN: 5188

South Asian (SAS) AF: 0.862 AC: 4155 AN: 4820

European-Finnish (FIN) AF: 0.698 AC: 7371 AN: 10566

Middle Eastern (MID) AF: 0.738 AC: 217 AN: 294

European-Non Finnish (NFE) AF: 0.738 AC: 50210 AN: 67996

Other (OTH) AF: 0.745 AC: 1573 AN: 2110

Alfa AF: 0.746 Hom.: 177634

Bravo AF: 0.776

Asia WGS AF: 0.907 AC: 3151 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	1.0
DANN	Benign	0.21
PhyloP100		-0.27
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: rs790631; hg19: chr1-67676922;