1-67225982-A-G

Variant names:

• chr1-67225982-A-G
• rs4655692
• NM_144701.3:c.955+6252A>G

Variant summary

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

The NM_144701.3(IL23R):​c.955+6252A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.761 in 152,158 control chromosomes in the GnomAD database, including 44,407 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 0.76 (44407 hom., cov: 33)
• Consequence: IL23R NM_144701.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.796
• 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 (EAS) allele frequency at 95% confidence interval = 0.963 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
IL23R	NM_144701.3	c.955+6252A>G		intron_variant	Intron 7 of 10	ENST00000347310.10	NP_653302.2
IL23R	XM_011540790.4	c.955+6252A>G		intron_variant	Intron 7 of 10		XP_011539092.1
IL23R	XM_011540791.4	c.955+6252A>G		intron_variant	Intron 7 of 10		XP_011539093.1
IL23R	XM_047447227.1	c.955+6252A>G		intron_variant	Intron 7 of 10		XP_047303183.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
IL23R	ENST00000347310.10	c.955+6252A>G		intron_variant	Intron 7 of 10	1	NM_144701.3	ENSP00000321345.5

Frequencies

GnomAD3 genomes AF: 0.761 AC: 115736 AN: 152040 Hom.: 44372 Cov.: 33

Gnomad AFR AF: 0.721

Gnomad AMI AF: 0.746

Gnomad AMR AF: 0.805

Gnomad ASJ AF: 0.767

Gnomad EAS AF: 0.986

Gnomad SAS AF: 0.865

Gnomad FIN AF: 0.708

Gnomad MID AF: 0.826

Gnomad NFE AF: 0.759

Gnomad OTH AF: 0.762

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

GnomAD4 genome AF: 0.761 AC: 115827 AN: 152158 Hom.: 44407 Cov.: 33 AF XY: 0.762 AC XY: 56702 AN XY: 74404

African (AFR) AF: 0.721 AC: 29951 AN: 41524

American (AMR) AF: 0.805 AC: 12306 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.767 AC: 2661 AN: 3470

East Asian (EAS) AF: 0.986 AC: 5109 AN: 5182

South Asian (SAS) AF: 0.864 AC: 4168 AN: 4824

European-Finnish (FIN) AF: 0.708 AC: 7490 AN: 10580

Middle Eastern (MID) AF: 0.830 AC: 244 AN: 294

European-Non Finnish (NFE) AF: 0.759 AC: 51606 AN: 67980

Other (OTH) AF: 0.764 AC: 1612 AN: 2110

Alfa AF: 0.749 Hom.: 5756

Bravo AF: 0.767

Asia WGS AF: 0.923 AC: 3207 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	0.26
DANN	Benign	0.48
PhyloP100		-0.80
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: rs4655692; hg19: chr1-67691665;