rs6671221

Variant names:

• chr1-67172608-T-C
• rs6671221
• NM_144701.3:c.367+2970T>C

Variant summary

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

The NM_144701.3(IL23R):​c.367+2970T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.469 in 152,022 control chromosomes in the GnomAD database, including 17,523 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 0.47 (17523 hom., cov: 32)
• Consequence: IL23R NM_144701.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0350
• Publications: 5 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=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.625 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.367+2970T>C		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.367+2970T>C		intron	N/A	ENSP00000321345.5
	IL23R	ENST00000637002.1	TSL:1	n.367+2970T>C		intron	N/A	ENSP00000490340.2
	IL23R	ENST00000697164.1		c.367+2970T>C		intron	N/A	ENSP00000513153.1

Frequencies

GnomAD3 genomes AF: 0.469 AC: 71242 AN: 151904 Hom.: 17521 Cov.: 32

Gnomad AFR AF: 0.333

Gnomad AMI AF: 0.647

Gnomad AMR AF: 0.396

Gnomad ASJ AF: 0.609

Gnomad EAS AF: 0.643

Gnomad SAS AF: 0.626

Gnomad FIN AF: 0.512

Gnomad MID AF: 0.535

Gnomad NFE AF: 0.528

Gnomad OTH AF: 0.445

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

GnomAD4 genome AF: 0.469 AC: 71248 AN: 152022 Hom.: 17523 Cov.: 32 AF XY: 0.470 AC XY: 34923 AN XY: 74284

African (AFR) AF: 0.333 AC: 13801 AN: 41502

American (AMR) AF: 0.396 AC: 6043 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.609 AC: 2113 AN: 3468

East Asian (EAS) AF: 0.643 AC: 3327 AN: 5176

South Asian (SAS) AF: 0.626 AC: 3014 AN: 4816

European-Finnish (FIN) AF: 0.512 AC: 5403 AN: 10554

Middle Eastern (MID) AF: 0.538 AC: 157 AN: 292

European-Non Finnish (NFE) AF: 0.528 AC: 35863 AN: 67924

Other (OTH) AF: 0.444 AC: 937 AN: 2110

Alfa AF: 0.486 Hom.: 2451

Bravo AF: 0.453

Asia WGS AF: 0.553 AC: 1921 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	1.7
DANN	Benign	0.57
PhyloP100		0.035
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: rs6671221; hg19: chr1-67638291;