rs11465754

chr1-67165748-A-Gchr1-67165748-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000637002.1(IL23R):c.-29-2344A>G variant causes a intron, NMD transcript 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, NMD_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.05

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

Verdict is Benign. Variant got -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/exons	MANE	UniProt
IL23R	XM_011540790.4	c.-29-2344A>G		intron_variant
IL23R	XM_011540791.4	c.-29-2344A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
IL23R	ENST00000637002.1	c.-29-2344A>G		intron_variant, NMD_transcript_variant		1
C1orf141	ENST00000371007.6	c.-103-34521T>C		intron_variant		5		P1
C1orf141	ENST00000448166.6	c.-103-34521T>C		intron_variant		5
IL23R	ENST00000697222.1	c.-29-2344A>G		intron_variant

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

Gnomad4 AFR AF: 0.462

Gnomad4 AMR AF: 0.481

Gnomad4 ASJ AF: 0.249

Gnomad4 EAS AF: 0.382

Gnomad4 SAS AF: 0.321

Gnomad4 FIN AF: 0.338

Gnomad4 NFE AF: 0.340

Gnomad4 OTH AF: 0.393

Alfa AF: 0.383 Hom.: 3826

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

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

Publications

LitVar

Other links and lift over

dbSNP: rs11465754; hg19: chr1-67631431;