rs747842

chr3-136984279-A-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_144717.4(IL20RB):c.406+1929A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.466 in 151,376 control chromosomes in the GnomAD database, including 16,923 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 0.47 (16923 hom., cov: 31)
• Consequence: IL20RB NM_144717.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.332

Genes affected

IL20RB (HGNC:6004): (interleukin 20 receptor subunit beta) IL20RB and IL20RA (MIM 605620) form a heterodimeric receptor for interleukin-20 (IL20; MIM 605619) (Blumberg et al., 2001 [PubMed 11163236]).[supplied by OMIM, Feb 2009]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.676 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
IL20RB	NM_144717.4	c.406+1929A>C		intron_variant		ENST00000329582.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
IL20RB	ENST00000329582.9	c.406+1929A>C		intron_variant		1	NM_144717.4	P1

Frequencies

GnomAD3 genomes AF: 0.466 AC: 70513 AN: 151256 Hom.: 16891 Cov.: 31

Gnomad AFR AF: 0.529

Gnomad AMI AF: 0.314

Gnomad AMR AF: 0.539

Gnomad ASJ AF: 0.387

Gnomad EAS AF: 0.694

Gnomad SAS AF: 0.391

Gnomad FIN AF: 0.371

Gnomad MID AF: 0.362

Gnomad NFE AF: 0.422

Gnomad OTH AF: 0.460

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

GnomAD4 genome AF: 0.466 AC: 70592 AN: 151376 Hom.: 16923 Cov.: 31 AF XY: 0.466 AC XY: 34435 AN XY: 73938

Gnomad4 AFR AF: 0.529

Gnomad4 AMR AF: 0.539

Gnomad4 ASJ AF: 0.387

Gnomad4 EAS AF: 0.695

Gnomad4 SAS AF: 0.394

Gnomad4 FIN AF: 0.371

Gnomad4 NFE AF: 0.422

Gnomad4 OTH AF: 0.460

Alfa AF: 0.427 Hom.: 6376

Bravo AF: 0.483

Asia WGS AF: 0.561 AC: 1952 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	1.8
Dann	Benign	0.50

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

Other links and lift over

dbSNP: rs747842; hg19: chr3-136703121;