rs4655684

Variant names:

• chr1-67146089-C-T
• rs4655684
• ENST00000637002.1:n.-30+6928C>T

Variant summary

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

The ENST00000697222.1(IL23R):​c.-30+6928C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.342 in 151,994 control chromosomes in the GnomAD database, including 9,084 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 0.34 (9084 hom., cov: 31)
• Consequence: IL23R ENST00000697222.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.661
• 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=-0.94).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.459 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000697222.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	IL23R	ENST00000637002.1	TSL:1	n.-30+6928C>T		intron	N/A	ENSP00000490340.2	A0A1B0GV19
	C1orf141	ENST00000371007.6	TSL:5	c.-103-14862G>A		intron	N/A	ENSP00000360046.1	Q5JVX7-1
	C1orf141	ENST00000448166.6	TSL:5	c.-103-14862G>A		intron	N/A	ENSP00000415519.2	Q5JVX6

Frequencies

GnomAD3 genomes AF: 0.341 AC: 51863 AN: 151876 Hom.: 9062 Cov.: 31

Gnomad AFR AF: 0.302

Gnomad AMI AF: 0.227

Gnomad AMR AF: 0.468

Gnomad ASJ AF: 0.252

Gnomad EAS AF: 0.374

Gnomad SAS AF: 0.323

Gnomad FIN AF: 0.345

Gnomad MID AF: 0.241

Gnomad NFE AF: 0.342

Gnomad OTH AF: 0.356

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

GnomAD4 genome AF: 0.342 AC: 51928 AN: 151994 Hom.: 9084 Cov.: 31 AF XY: 0.343 AC XY: 25482 AN XY: 74276

African (AFR) AF: 0.302 AC: 12503 AN: 41424

American (AMR) AF: 0.468 AC: 7155 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.252 AC: 875 AN: 3470

East Asian (EAS) AF: 0.373 AC: 1927 AN: 5164

South Asian (SAS) AF: 0.322 AC: 1553 AN: 4816

European-Finnish (FIN) AF: 0.345 AC: 3641 AN: 10550

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

European-Non Finnish (NFE) AF: 0.342 AC: 23236 AN: 67964

Other (OTH) AF: 0.358 AC: 758 AN: 2116

Alfa AF: 0.350 Hom.: 1743

Bravo AF: 0.351

Asia WGS AF: 0.402 AC: 1395 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.77
DANN	Benign	0.12
PhyloP100		-0.66
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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs4655684;

hg19: chr1-67611772;