3-136981707-C-A

Variant names:

• chr3-136981707-C-A
• rs75977
• NM_144717.4:c.216-453C>A

Variant summary

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

The NM_144717.4(IL20RB):​c.216-453C>A 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 152,010 control chromosomes in the GnomAD database, including 16,990 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 (16990 hom., cov: 33)
• Consequence: IL20RB NM_144717.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.346
• Publications: 4 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=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.681 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
IL20RB	NM_144717.4	c.216-453C>A		intron_variant	Intron 2 of 6	ENST00000329582.9	NP_653318.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
IL20RB	ENST00000329582.9	c.216-453C>A		intron_variant	Intron 2 of 6	1	NM_144717.4	ENSP00000328133.4

Frequencies

GnomAD3 genomes AF: 0.465 AC: 70696 AN: 151892 Hom.: 16959 Cov.: 33

Gnomad AFR AF: 0.525

Gnomad AMI AF: 0.317

Gnomad AMR AF: 0.538

Gnomad ASJ AF: 0.387

Gnomad EAS AF: 0.699

Gnomad SAS AF: 0.390

Gnomad FIN AF: 0.370

Gnomad MID AF: 0.361

Gnomad NFE AF: 0.422

Gnomad OTH AF: 0.459

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

GnomAD4 genome AF: 0.466 AC: 70766 AN: 152010 Hom.: 16990 Cov.: 33 AF XY: 0.465 AC XY: 34541 AN XY: 74268

African (AFR) AF: 0.524 AC: 21756 AN: 41484

American (AMR) AF: 0.539 AC: 8232 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.387 AC: 1342 AN: 3466

East Asian (EAS) AF: 0.700 AC: 3617 AN: 5168

South Asian (SAS) AF: 0.392 AC: 1887 AN: 4814

European-Finnish (FIN) AF: 0.370 AC: 3895 AN: 10532

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

European-Non Finnish (NFE) AF: 0.422 AC: 28678 AN: 67968

Other (OTH) AF: 0.459 AC: 968 AN: 2108

Alfa AF: 0.401 Hom.: 5976

Bravo AF: 0.481

Asia WGS AF: 0.561 AC: 1949 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	2.3
DANN	Benign	0.58
PhyloP100		0.35
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs75977; hg19: chr3-136700549;