chr3-136957461-C-T

Variant names:

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

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
IL20RB-AS1	NR_183727.1	n.417+1804G>A		intron_variant	Intron 2 of 2
IL20RB-AS1	NR_183728.1	n.463-11130G>A		intron_variant	Intron 2 of 2
IL20RB-AS1	NR_183729.1	n.463-2670G>A		intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
IL20RB	ENST00000484501.1	n.67-434C>T		intron_variant	Intron 1 of 2	4

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

Gnomad4 AFR AF: 0.518

Gnomad4 AMR AF: 0.538

Gnomad4 ASJ AF: 0.387

Gnomad4 EAS AF: 0.696

Gnomad4 SAS AF: 0.394

Gnomad4 FIN AF: 0.369

Gnomad4 NFE AF: 0.422

Gnomad4 OTH AF: 0.455

Alfa AF: 0.425 Hom.: 18942

Bravo AF: 0.478

Asia WGS AF: 0.560 AC: 1945 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs835634; hg19: chr3-136676303;