chr1-67193120-G-A

Variant names:

• chr1-67193120-G-A
• rs72676067
• NM_144701.3:c.492-7617G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_144701.3(IL23R):​c.492-7617G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.297 in 151,974 control chromosomes in the GnomAD database, including 7,091 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 0.30 (7091 hom., cov: 32)
• Consequence: IL23R NM_144701.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.399
• Publications: 7 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=-0.81).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.422 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_144701.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	IL23R	NM_144701.3	MANE Select	c.492-7617G>A		intron	N/A	NP_653302.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	IL23R	ENST00000347310.10	TSL:1 MANE Select	c.492-7617G>A		intron	N/A	ENSP00000321345.5
	IL23R	ENST00000637002.1	TSL:1	n.492-7622G>A		intron	N/A	ENSP00000490340.2
	IL23R	ENST00000697164.1		c.492-7617G>A		intron	N/A	ENSP00000513153.1

Frequencies

GnomAD3 genomes AF: 0.297 AC: 45102 AN: 151856 Hom.: 7075 Cov.: 32

Gnomad AFR AF: 0.219

Gnomad AMI AF: 0.271

Gnomad AMR AF: 0.430

Gnomad ASJ AF: 0.177

Gnomad EAS AF: 0.364

Gnomad SAS AF: 0.289

Gnomad FIN AF: 0.338

Gnomad MID AF: 0.209

Gnomad NFE AF: 0.310

Gnomad OTH AF: 0.311

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

GnomAD4 genome AF: 0.297 AC: 45157 AN: 151974 Hom.: 7091 Cov.: 32 AF XY: 0.300 AC XY: 22311 AN XY: 74266

African (AFR) AF: 0.219 AC: 9066 AN: 41432

American (AMR) AF: 0.431 AC: 6580 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.177 AC: 614 AN: 3468

East Asian (EAS) AF: 0.364 AC: 1883 AN: 5172

South Asian (SAS) AF: 0.289 AC: 1391 AN: 4814

European-Finnish (FIN) AF: 0.338 AC: 3568 AN: 10554

Middle Eastern (MID) AF: 0.211 AC: 62 AN: 294

European-Non Finnish (NFE) AF: 0.310 AC: 21084 AN: 67952

Other (OTH) AF: 0.314 AC: 662 AN: 2110

Alfa AF: 0.301 Hom.: 3065

Bravo AF: 0.302

Asia WGS AF: 0.366 AC: 1272 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	6.8
DANN	Benign	0.74
PhyloP100		0.40
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: rs72676067; hg19: chr1-67658803;