rs4655683

Variant names:

• chr1-67145930-G-A
• rs4655683
• ENST00000637002.1:n.-30+6769G>A

Your query was ambiguous. Multiple possible variants found:

• chr1-67145930-G-A
• chr1-67145930-G-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+6769G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.374 in 151,988 control chromosomes in the GnomAD database, including 10,807 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 0.37 (10807 hom., cov: 32)
• Consequence: IL23R ENST00000697222.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.293
• Publications: 14 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=-1.01).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.471 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+6769G>A		intron	N/A	ENSP00000490340.2	A0A1B0GV19
	C1orf141	ENST00000371007.6	TSL:5	c.-103-14703C>T		intron	N/A	ENSP00000360046.1	Q5JVX7-1
	C1orf141	ENST00000448166.6	TSL:5	c.-103-14703C>T		intron	N/A	ENSP00000415519.2	Q5JVX6

Frequencies

GnomAD3 genomes AF: 0.373 AC: 56711 AN: 151870 Hom.: 10780 Cov.: 32

Gnomad AFR AF: 0.412

Gnomad AMI AF: 0.225

Gnomad AMR AF: 0.480

Gnomad ASJ AF: 0.253

Gnomad EAS AF: 0.374

Gnomad SAS AF: 0.323

Gnomad FIN AF: 0.345

Gnomad MID AF: 0.244

Gnomad NFE AF: 0.342

Gnomad OTH AF: 0.379

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

GnomAD4 genome AF: 0.374 AC: 56789 AN: 151988 Hom.: 10807 Cov.: 32 AF XY: 0.374 AC XY: 27803 AN XY: 74292

African (AFR) AF: 0.413 AC: 17105 AN: 41454

American (AMR) AF: 0.480 AC: 7335 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.253 AC: 877 AN: 3470

East Asian (EAS) AF: 0.373 AC: 1926 AN: 5158

South Asian (SAS) AF: 0.322 AC: 1552 AN: 4814

European-Finnish (FIN) AF: 0.345 AC: 3646 AN: 10572

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

European-Non Finnish (NFE) AF: 0.342 AC: 23264 AN: 67928

Other (OTH) AF: 0.381 AC: 806 AN: 2114

Alfa AF: 0.354 Hom.: 16972

Bravo AF: 0.387

Asia WGS AF: 0.409 AC: 1420 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.3
DANN	Benign	0.64
PhyloP100		0.29
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: rs4655683;

hg19: chr1-67611613;