1-67165579-C-T

Variant names:

• chr1-67165579-C-T
• rs6682925
• ENST00000637002.1:n.-29-2513C>T

Variant summary

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

The ENST00000697222.1(IL23R):​c.-29-2513C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.471 in 151,948 control chromosomes in the GnomAD database, including 17,711 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 (17711 hom., cov: 32)
• Consequence: IL23R ENST00000697222.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.163
• Publications: 36 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=-0.97).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.612 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000697222.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	IL23R	ENST00000637002.1	TSL:1	n.-29-2513C>T		intron	N/A	ENSP00000490340.2	A0A1B0GV19
	C1orf141	ENST00000371007.6	TSL:5	c.-103-34352G>A		intron	N/A	ENSP00000360046.1	Q5JVX7-1
	C1orf141	ENST00000448166.6	TSL:5	c.-103-34352G>A		intron	N/A	ENSP00000415519.2	Q5JVX6

Frequencies

GnomAD3 genomes AF: 0.472 AC: 71619 AN: 151830 Hom.: 17710 Cov.: 32

Gnomad AFR AF: 0.332

Gnomad AMI AF: 0.647

Gnomad AMR AF: 0.397

Gnomad ASJ AF: 0.611

Gnomad EAS AF: 0.613

Gnomad SAS AF: 0.631

Gnomad FIN AF: 0.519

Gnomad MID AF: 0.541

Gnomad NFE AF: 0.535

Gnomad OTH AF: 0.446

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

GnomAD4 genome AF: 0.471 AC: 71626 AN: 151948 Hom.: 17711 Cov.: 32 AF XY: 0.472 AC XY: 35075 AN XY: 74270

African (AFR) AF: 0.331 AC: 13726 AN: 41426

American (AMR) AF: 0.397 AC: 6062 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.611 AC: 2118 AN: 3468

East Asian (EAS) AF: 0.613 AC: 3170 AN: 5168

South Asian (SAS) AF: 0.631 AC: 3039 AN: 4816

European-Finnish (FIN) AF: 0.519 AC: 5467 AN: 10538

Middle Eastern (MID) AF: 0.544 AC: 160 AN: 294

European-Non Finnish (NFE) AF: 0.535 AC: 36356 AN: 67954

Other (OTH) AF: 0.445 AC: 939 AN: 2108

Alfa AF: 0.436 Hom.: 3919

Bravo AF: 0.454

Asia WGS AF: 0.549 AC: 1912 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.1
DANN	Benign	0.62
PhyloP100		-0.16
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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs6682925;

hg19: chr1-67631262;