chr1-67165748-A-G

Variant names:

• chr1-67165748-A-G
• rs11465754
• ENST00000637002.1:n.-29-2344A>G

Variant summary

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

The ENST00000637002.1(IL23R):​n.-29-2344A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.386 in 151,908 control chromosomes in the GnomAD database, including 11,701 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 0.39 (11701 hom., cov: 33)
• Consequence: IL23R ENST00000637002.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.05
• 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=-0.93).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.472 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
IL23R	XM_011540790.4	c.-29-2344A>G		intron_variant	Intron 1 of 10		XP_011539092.1
IL23R	XM_011540791.4	c.-29-2344A>G		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.-29-2344A>G		intron_variant	Intron 1 of 10	1		ENSP00000490340.2
C1orf141	ENST00000371007.6	c.-103-34521T>C		intron_variant	Intron 1 of 7	5		ENSP00000360046.1
C1orf141	ENST00000448166.6	c.-103-34521T>C		intron_variant	Intron 1 of 9	5		ENSP00000415519.2
IL23R	ENST00000697222.1	c.-29-2344A>G		intron_variant	Intron 1 of 2			ENSP00000513189.1

Frequencies

GnomAD3 genomes AF: 0.386 AC: 58608 AN: 151786 Hom.: 11667 Cov.: 33

Gnomad AFR AF: 0.462

Gnomad AMI AF: 0.280

Gnomad AMR AF: 0.481

Gnomad ASJ AF: 0.249

Gnomad EAS AF: 0.382

Gnomad SAS AF: 0.322

Gnomad FIN AF: 0.338

Gnomad MID AF: 0.242

Gnomad NFE AF: 0.340

Gnomad OTH AF: 0.391

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

GnomAD4 genome AF: 0.386 AC: 58699 AN: 151908 Hom.: 11701 Cov.: 33 AF XY: 0.387 AC XY: 28704 AN XY: 74250

African (AFR) AF: 0.462 AC: 19159 AN: 41456

American (AMR) AF: 0.481 AC: 7333 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.249 AC: 863 AN: 3466

East Asian (EAS) AF: 0.382 AC: 1976 AN: 5170

South Asian (SAS) AF: 0.321 AC: 1545 AN: 4820

European-Finnish (FIN) AF: 0.338 AC: 3563 AN: 10526

Middle Eastern (MID) AF: 0.248 AC: 73 AN: 294

European-Non Finnish (NFE) AF: 0.340 AC: 23103 AN: 67918

Other (OTH) AF: 0.393 AC: 831 AN: 2112

Alfa AF: 0.383 Hom.: 4742

Bravo AF: 0.403

Asia WGS AF: 0.414 AC: 1438 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.32
DANN	Benign	0.30
PhyloP100		-1.1
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: rs11465754; hg19: chr1-67631431;