Variant rs1004819 details in Genebe, Genetics Data Aggregator

Variant summary

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

The NM_144701.3(IL23R):c.653-2380G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.309 in 151872 control chromosomes in the gnomAD Genomes database, including 7718 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 0.31 ( 7718 hom., cov: 32)

Consequence

IL23R
NM_144701.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.372

Links

IL23R (HGNC:19100):

C1orf141 (HGNC:32044):

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.9).

BA1

GnomAd highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.557 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	MANE
IL23R	NM_144701.3 linkuse as main transcript	c.653-2380G>A	intron_variant	ENST00000347310.10
IL23R	XM_011540790.4 linkuse as main transcript	c.653-2380G>A	intron_variant
IL23R	XM_011540791.4 linkuse as main transcript	c.653-2380G>A	intron_variant
IL23R	XM_047447227.1 linkuse as main transcript	c.653-2380G>A	intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
IL23R	ENST00000347310.10 linkuse as main transcript	c.653-2380G>A		intron_variant		1	NM_144701.3	P1	Q5VWK5-1

Frequencies

GnomAD3 genomes

AF:

0.309

AC:

46884

AN:

151872

Hom.:

7718

Cov.:

show subpopulations

Gnomad AFR

AF:

0.297

Gnomad AMI

AF:

0.331

Gnomad AMR

AF:

0.247

Gnomad ASJ

AF:

0.342

Gnomad EAS

AF:

0.574

Gnomad SAS

AF:

0.565

Gnomad FIN

AF:

0.263

Gnomad MID

AF:

0.446

Gnomad NFE

AF:

0.296

Gnomad OTH

AF:

0.311

Alfa

AF:

0.306

Hom.:

10965

Bravo

AF:

0.302

Asia WGS

AF:

0.500

AC:

1737

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

Cadd

Benign

3.7

Dann

Benign

0.41

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

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