3-136957461-C-T

Variant names:

• chr3-136957461-C-T
• rs835634
• ENST00000484501.1:n.67-434C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000484501.1(IL20RB):​n.67-434C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.463 in 151,894 control chromosomes in the GnomAD database, including 16,808 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 0.46 (16808 hom., cov: 32)
• Consequence: IL20RB ENST00000484501.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.19
• Publications: 9 publications found

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]

IL20RB-AS1 (HGNC:40298): (IL20RB antisense RNA 1)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.677 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000484501.1. 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
	IL20RB-AS1	NR_183727.1		n.417+1804G>A		intron	N/A
	IL20RB-AS1	NR_183728.1		n.463-11130G>A		intron	N/A
	IL20RB-AS1	NR_183729.1		n.463-2670G>A		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	IL20RB	ENST00000484501.1	TSL:4	n.67-434C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.463 AC: 70301 AN: 151776 Hom.: 16775 Cov.: 32

Gnomad AFR AF: 0.519

Gnomad AMI AF: 0.317

Gnomad AMR AF: 0.537

Gnomad ASJ AF: 0.387

Gnomad EAS AF: 0.695

Gnomad SAS AF: 0.392

Gnomad FIN AF: 0.369

Gnomad MID AF: 0.361

Gnomad NFE AF: 0.422

Gnomad OTH AF: 0.455

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

GnomAD4 genome AF: 0.463 AC: 70371 AN: 151894 Hom.: 16808 Cov.: 32 AF XY: 0.463 AC XY: 34352 AN XY: 74220

African (AFR) AF: 0.518 AC: 21454 AN: 41408

American (AMR) AF: 0.538 AC: 8208 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.387 AC: 1342 AN: 3468

East Asian (EAS) AF: 0.696 AC: 3591 AN: 5160

South Asian (SAS) AF: 0.394 AC: 1897 AN: 4812

European-Finnish (FIN) AF: 0.369 AC: 3882 AN: 10524

Middle Eastern (MID) AF: 0.354 AC: 104 AN: 294

European-Non Finnish (NFE) AF: 0.422 AC: 28644 AN: 67942

Other (OTH) AF: 0.455 AC: 960 AN: 2108

Alfa AF: 0.428 Hom.: 22108

Bravo AF: 0.478

Asia WGS AF: 0.560 AC: 1945 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.17
DANN	Benign	0.58
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs835634; hg19: chr3-136676303;