chr1-67215986-T-G

Variant names:

• chr1-67215986-T-G
• rs7517847
• NM_144701.3:c.799-3588T>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.799-3588T>G 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 152,046 control chromosomes in the GnomAD database, including 11,698 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 (11698 hom., cov: 32)
• Consequence: IL23R NM_144701.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.366
• Publications: 189 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 = 0.523 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_144701.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	IL23R	NM_144701.3	MANE Select	c.799-3588T>G		intron	N/A	NP_653302.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	IL23R	ENST00000347310.10	TSL:1 MANE Select	c.799-3588T>G		intron	N/A	ENSP00000321345.5
	IL23R	ENST00000425614.3	TSL:1	c.34-3588T>G		intron	N/A	ENSP00000387640.2
	IL23R	ENST00000473881.2	TSL:1	n.34-3588T>G		intron	N/A	ENSP00000486667.1

Frequencies

GnomAD3 genomes AF: 0.374 AC: 56787 AN: 151928 Hom.: 11683 Cov.: 32

Gnomad AFR AF: 0.199

Gnomad AMI AF: 0.422

Gnomad AMR AF: 0.532

Gnomad ASJ AF: 0.330

Gnomad EAS AF: 0.438

Gnomad SAS AF: 0.298

Gnomad FIN AF: 0.433

Gnomad MID AF: 0.259

Gnomad NFE AF: 0.438

Gnomad OTH AF: 0.368

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

GnomAD4 genome AF: 0.374 AC: 56827 AN: 152046 Hom.: 11698 Cov.: 32 AF XY: 0.376 AC XY: 27918 AN XY: 74306

African (AFR) AF: 0.199 AC: 8244 AN: 41496

American (AMR) AF: 0.533 AC: 8128 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.330 AC: 1145 AN: 3472

East Asian (EAS) AF: 0.438 AC: 2266 AN: 5174

South Asian (SAS) AF: 0.297 AC: 1431 AN: 4814

European-Finnish (FIN) AF: 0.433 AC: 4571 AN: 10556

Middle Eastern (MID) AF: 0.272 AC: 80 AN: 294

European-Non Finnish (NFE) AF: 0.438 AC: 29795 AN: 67960

Other (OTH) AF: 0.370 AC: 783 AN: 2114

Alfa AF: 0.413 Hom.: 57409

Bravo AF: 0.379

Asia WGS AF: 0.403 AC: 1401 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	1.9
DANN	Benign	0.62
PhyloP100		-0.37
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: rs7517847; hg19: chr1-67681669;