rs7528924

Variant names:

• chr1-67223353-G-A
• rs7528924
• NM_144701.3:c.955+3623G>A

Your query was ambiguous. Multiple possible variants found:

• chr1-67223353-G-A
• chr1-67223353-G-C
• chr1-67223353-G-T

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+3623G>A 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 152,128 control chromosomes in the GnomAD database, including 44,428 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 (44428 hom., cov: 32)
• Consequence: IL23R NM_144701.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.71
• Publications: 13 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=-0.96).
• 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+3623G>A		intron_variant	Intron 7 of 10	ENST00000347310.10	NP_653302.2
IL23R	XM_011540790.4	c.955+3623G>A		intron_variant	Intron 7 of 10		XP_011539092.1
IL23R	XM_011540791.4	c.955+3623G>A		intron_variant	Intron 7 of 10		XP_011539093.1
IL23R	XM_047447227.1	c.955+3623G>A		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+3623G>A		intron_variant	Intron 7 of 10	1	NM_144701.3	ENSP00000321345.5

Frequencies

GnomAD3 genomes AF: 0.761 AC: 115754 AN: 152012 Hom.: 44393 Cov.: 32

Gnomad AFR AF: 0.722

Gnomad AMI AF: 0.746

Gnomad AMR AF: 0.805

Gnomad ASJ AF: 0.767

Gnomad EAS AF: 0.986

Gnomad SAS AF: 0.864

Gnomad FIN AF: 0.708

Gnomad MID AF: 0.826

Gnomad NFE AF: 0.759

Gnomad OTH AF: 0.761

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

GnomAD4 genome AF: 0.761 AC: 115845 AN: 152128 Hom.: 44428 Cov.: 32 AF XY: 0.762 AC XY: 56693 AN XY: 74382

African (AFR) AF: 0.722 AC: 29935 AN: 41476

American (AMR) AF: 0.805 AC: 12319 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.767 AC: 2662 AN: 3472

East Asian (EAS) AF: 0.986 AC: 5115 AN: 5188

South Asian (SAS) AF: 0.864 AC: 4170 AN: 4826

European-Finnish (FIN) AF: 0.708 AC: 7471 AN: 10554

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

European-Non Finnish (NFE) AF: 0.759 AC: 51638 AN: 68000

Other (OTH) AF: 0.763 AC: 1611 AN: 2112

Alfa AF: 0.762 Hom.: 115027

Bravo AF: 0.767

Asia WGS AF: 0.922 AC: 3204 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.066
DANN	Benign	0.44
PhyloP100		-1.7
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: rs7528924; hg19: chr1-67689036;