chr1-67165650-C-T

Variant names:

• chr1-67165650-C-T
• rs6683039
• ENST00000637002.1:n.-29-2442C>T

Variant summary

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

The ENST00000637002.1(IL23R):​n.-29-2442C>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 152,102 control chromosomes in the GnomAD database, including 17,719 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 (17719 hom., cov: 33)
• Consequence: IL23R ENST00000637002.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.26
• Publications: 6 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=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.612 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
IL23R	XM_011540790.4	c.-29-2442C>T		intron_variant	Intron 1 of 10		XP_011539092.1
IL23R	XM_011540791.4	c.-29-2442C>T		intron_variant	Intron 1 of 10		XP_011539093.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
IL23R	ENST00000637002.1	n.-29-2442C>T		intron_variant	Intron 1 of 10	1		ENSP00000490340.2
C1orf141	ENST00000371007.6	c.-103-34423G>A		intron_variant	Intron 1 of 7	5		ENSP00000360046.1
C1orf141	ENST00000448166.6	c.-103-34423G>A		intron_variant	Intron 1 of 9	5		ENSP00000415519.2
IL23R	ENST00000697222.1	c.-29-2442C>T		intron_variant	Intron 1 of 2			ENSP00000513189.1

Frequencies

GnomAD3 genomes AF: 0.471 AC: 71641 AN: 151984 Hom.: 17718 Cov.: 33

Gnomad AFR AF: 0.331

Gnomad AMI AF: 0.647

Gnomad AMR AF: 0.397

Gnomad ASJ AF: 0.610

Gnomad EAS AF: 0.612

Gnomad SAS AF: 0.631

Gnomad FIN AF: 0.517

Gnomad MID AF: 0.541

Gnomad NFE AF: 0.535

Gnomad OTH AF: 0.445

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

GnomAD4 genome AF: 0.471 AC: 71648 AN: 152102 Hom.: 17719 Cov.: 33 AF XY: 0.472 AC XY: 35083 AN XY: 74350

African (AFR) AF: 0.331 AC: 13736 AN: 41504

American (AMR) AF: 0.397 AC: 6062 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.610 AC: 2118 AN: 3470

East Asian (EAS) AF: 0.612 AC: 3160 AN: 5160

South Asian (SAS) AF: 0.630 AC: 3042 AN: 4826

European-Finnish (FIN) AF: 0.517 AC: 5466 AN: 10570

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

European-Non Finnish (NFE) AF: 0.535 AC: 36376 AN: 67984

Other (OTH) AF: 0.445 AC: 939 AN: 2112

Alfa AF: 0.462 Hom.: 4055

Bravo AF: 0.454

Asia WGS AF: 0.549 AC: 1913 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.33
DANN	Benign	0.71
PhyloP100		-2.3
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: rs6683039; hg19: chr1-67631333;