1-67236082-G-T

Variant names:

• chr1-67236082-G-T
• rs12030948
• NM_144701.3:c.956-631G>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.956-631G>T 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 152,032 control chromosomes in the GnomAD database, including 9,759 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 (9759 hom., cov: 32)
• Consequence: IL23R NM_144701.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.837
• Publications: 10 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=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.705 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
IL23R	NM_144701.3	c.956-631G>T		intron_variant	Intron 7 of 10	ENST00000347310.10	NP_653302.2
IL23R	XM_011540790.4	c.956-631G>T		intron_variant	Intron 7 of 10		XP_011539092.1
IL23R	XM_011540791.4	c.956-631G>T		intron_variant	Intron 7 of 10		XP_011539093.1
IL23R	XM_047447227.1	c.956-631G>T		intron_variant	Intron 7 of 10		XP_047303183.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
IL23R	ENST00000347310.10	c.956-631G>T		intron_variant	Intron 7 of 10	1	NM_144701.3	ENSP00000321345.5

Frequencies

GnomAD3 genomes AF: 0.338 AC: 51306 AN: 151914 Hom.: 9749 Cov.: 32

Gnomad AFR AF: 0.203

Gnomad AMI AF: 0.409

Gnomad AMR AF: 0.328

Gnomad ASJ AF: 0.435

Gnomad EAS AF: 0.724

Gnomad SAS AF: 0.600

Gnomad FIN AF: 0.339

Gnomad MID AF: 0.541

Gnomad NFE AF: 0.366

Gnomad OTH AF: 0.366

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

GnomAD4 genome AF: 0.338 AC: 51340 AN: 152032 Hom.: 9759 Cov.: 32 AF XY: 0.343 AC XY: 25451 AN XY: 74306

African (AFR) AF: 0.203 AC: 8421 AN: 41468

American (AMR) AF: 0.328 AC: 5008 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.435 AC: 1508 AN: 3468

East Asian (EAS) AF: 0.724 AC: 3738 AN: 5162

South Asian (SAS) AF: 0.602 AC: 2903 AN: 4826

European-Finnish (FIN) AF: 0.339 AC: 3579 AN: 10560

Middle Eastern (MID) AF: 0.534 AC: 157 AN: 294

European-Non Finnish (NFE) AF: 0.366 AC: 24879 AN: 67958

Other (OTH) AF: 0.368 AC: 776 AN: 2110

Alfa AF: 0.357 Hom.: 17284

Bravo AF: 0.330

Asia WGS AF: 0.588 AC: 2041 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	6.1
DANN	Benign	0.53
PhyloP100		0.84
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: rs12030948; hg19: chr1-67701765;