3-137011043-C-T

Variant summary

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

The NM_144717.4(IL20RB):c.*820C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.598 in 151,844 control chromosomes in the GnomAD database, including 27,629 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 0.60 (27628 hom., cov: 31)
  • Exomes 𝑓: 0.67 (1 hom.)
• Consequence: IL20RB NM_144717.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.199

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=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.884 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
IL20RB	NM_144717.4	c.*820C>T		3_prime_UTR_variant	7/7	ENST00000329582.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
IL20RB	ENST00000329582.9	c.*820C>T		3_prime_UTR_variant	7/7	1	NM_144717.4	P1
IL20RB	ENST00000475972.1	c.*1388C>T		3_prime_UTR_variant, NMD_transcript_variant	7/7	1
IL20RB	ENST00000469964.5	c.*1590C>T		3_prime_UTR_variant, NMD_transcript_variant	6/6	2

Frequencies

GnomAD3 genomes AF: 0.598 AC: 90670 AN: 151720 Hom.: 27600 Cov.: 31

Gnomad AFR AF: 0.548

Gnomad AMI AF: 0.593

Gnomad AMR AF: 0.657

Gnomad ASJ AF: 0.522

Gnomad EAS AF: 0.905

Gnomad SAS AF: 0.602

Gnomad FIN AF: 0.680

Gnomad MID AF: 0.490

Gnomad NFE AF: 0.583

Gnomad OTH AF: 0.581

GnomAD4 exome AF: 0.667 AC: 4 AN: 6 Hom.: 1 Cov.: 0 AF XY: 0.500 AC XY: 2 AN XY: 4

Gnomad4 NFE exome AF: 0.667

GnomAD4 genome AF: 0.598 AC: 90746 AN: 151838 Hom.: 27628 Cov.: 31 AF XY: 0.603 AC XY: 44790 AN XY: 74218

Gnomad4 AFR AF: 0.548

Gnomad4 AMR AF: 0.657

Gnomad4 ASJ AF: 0.522

Gnomad4 EAS AF: 0.905

Gnomad4 SAS AF: 0.604

Gnomad4 FIN AF: 0.680

Gnomad4 NFE AF: 0.583

Gnomad4 OTH AF: 0.587

Alfa AF: 0.579 Hom.: 4013

Bravo AF: 0.594

Asia WGS AF: 0.765 AC: 2657 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
Cadd	Benign	5.2
Dann	Benign	0.71

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: rs108858; hg19: chr3-136729885;