rs10889677

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_144701(IL23R):c.*309C>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.285 in 151888 control chromosomes in the gnomAD Genomes database, including 7310 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 0.28 ( 7310 hom., cov: 32)

Consequence

IL23R
NM_144701 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.209

Links

IL23R (HGNC:19100):

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.77).

BA1

GnomAd highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.704 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	#exon/exons	MANE
IL23R	NM_144701.3 linkuse as main transcript	c.*309C>A	3_prime_UTR_variant	11/11	ENST00000347310.10
IL23R	XM_011540790.4 linkuse as main transcript	c.*309C>A	3_prime_UTR_variant	11/11
IL23R	XM_011540791.4 linkuse as main transcript	c.*309C>A	3_prime_UTR_variant	11/11
IL23R	XM_047447227.1 linkuse as main transcript	c.1239+3510C>A	intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
IL23R	ENST00000347310.10 linkuse as main transcript	c.*309C>A		3_prime_UTR_variant	11/11	1	NM_144701.3	P1	Q5VWK5-1
IL23R	ENST00000473881.2 linkuse as main transcript	c.*1025C>A		3_prime_UTR_variant, NMD_transcript_variant	4/4	1

Frequencies

GnomAD3 genomes

AF:

0.285

AC:

43213

AN:

151888

Hom.:

7310

Cov.:

show subpopulations

Gnomad AFR

AF:

0.159

Gnomad AMI

AF:

0.310

Gnomad AMR

AF:

0.267

Gnomad ASJ

AF:

0.344

Gnomad EAS

AF:

0.724

Gnomad SAS

AF:

0.589

Gnomad FIN

AF:

0.293

Gnomad MID

AF:

0.443

Gnomad NFE

AF:

0.304

Gnomad OTH

AF:

0.308

GnomAD4 exome

AF:

0.355

AC:

74117

AN:

208754

Hom.:

15257

AF XY:

0.373

AC XY:

41629

AN XY:

111556

show subpopulations

Gnomad4 AFR exome

AF:

0.155

Gnomad4 AMR exome

AF:

0.286

Gnomad4 ASJ exome

AF:

0.352

Gnomad4 EAS exome

AF:

0.709

Gnomad4 SAS exome

AF:

0.554

Gnomad4 FIN exome

AF:

0.272

Gnomad4 NFE exome

AF:

0.304

Gnomad4 OTH exome

AF:

0.334

Alfa

AF:

0.321

Hom.:

17493

Bravo

AF:

0.274

Asia WGS

AF:

0.579

AC:

2007

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.77

Cadd

Benign

2.4

Dann

Benign

0.89

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Links

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over