1-67213310-T-C

Variant names:

• chr1-67213310-T-C
• rs790633
• NM_144701.3:c.798+6255T>C

Variant summary

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

The NM_144701.3(IL23R):​c.798+6255T>C 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 152,102 control chromosomes in the GnomAD database, including 45,629 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 (45629 hom., cov: 32)
• Consequence: IL23R NM_144701.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.72

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• 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+6255T>C		intron_variant	Intron 6 of 10	ENST00000347310.10	NP_653302.2
IL23R	XM_011540790.4	c.798+6255T>C		intron_variant	Intron 6 of 10		XP_011539092.1
IL23R	XM_011540791.4	c.798+6255T>C		intron_variant	Intron 6 of 10		XP_011539093.1
IL23R	XM_047447227.1	c.798+6255T>C		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+6255T>C		intron_variant	Intron 6 of 10	1	NM_144701.3	ENSP00000321345.5

Frequencies

GnomAD3 genomes AF: 0.770 AC: 116964 AN: 151984 Hom.: 45581 Cov.: 32

Gnomad AFR AF: 0.867

Gnomad AMI AF: 0.745

Gnomad AMR AF: 0.774

Gnomad ASJ AF: 0.656

Gnomad EAS AF: 0.970

Gnomad SAS AF: 0.860

Gnomad FIN AF: 0.675

Gnomad MID AF: 0.731

Gnomad NFE AF: 0.709

Gnomad OTH AF: 0.741

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

GnomAD4 genome AF: 0.770 AC: 117067 AN: 152102 Hom.: 45629 Cov.: 32 AF XY: 0.769 AC XY: 57163 AN XY: 74338

Gnomad4 AFR AF: 0.867

Gnomad4 AMR AF: 0.775

Gnomad4 ASJ AF: 0.656

Gnomad4 EAS AF: 0.970

Gnomad4 SAS AF: 0.859

Gnomad4 FIN AF: 0.675

Gnomad4 NFE AF: 0.709

Gnomad4 OTH AF: 0.743

Alfa AF: 0.722 Hom.: 5369

Bravo AF: 0.780

Asia WGS AF: 0.906 AC: 3149 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.67
DANN	Benign	0.38
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.0

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: rs790633; hg19: chr1-67678993;