3-136982453-G-T

Variant names:

• chr3-136982453-G-T
• rs361239
• NM_144717.4:c.406+103G>T

Variant summary

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

The NM_144717.4(IL20RB):​c.406+103G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.436 in 843,998 control chromosomes in the GnomAD database, including 82,899 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 (17011 hom., cov: 33)
  • Exomes 𝑓: 0.43 (65888 hom.)
• Consequence: IL20RB NM_144717.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0620
• 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]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.68 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
IL20RB	NM_144717.4	c.406+103G>T		intron_variant	Intron 3 of 6	ENST00000329582.9	NP_653318.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
IL20RB	ENST00000329582.9	c.406+103G>T		intron_variant	Intron 3 of 6	1	NM_144717.4	ENSP00000328133.4

Frequencies

GnomAD3 genomes AF: 0.465 AC: 70726 AN: 151950 Hom.: 16980 Cov.: 33

Gnomad AFR AF: 0.525

Gnomad AMI AF: 0.318

Gnomad AMR AF: 0.538

Gnomad ASJ AF: 0.387

Gnomad EAS AF: 0.698

Gnomad SAS AF: 0.391

Gnomad FIN AF: 0.369

Gnomad MID AF: 0.361

Gnomad NFE AF: 0.422

Gnomad OTH AF: 0.459

GnomAD4 exome AF: 0.430 AC: 297280 AN: 691928 Hom.: 65888 AF XY: 0.427 AC XY: 149834 AN XY: 351288

African (AFR) AF: 0.524 AC: 8966 AN: 17124

American (AMR) AF: 0.561 AC: 11099 AN: 19780

Ashkenazi Jewish (ASJ) AF: 0.367 AC: 5206 AN: 14202

East Asian (EAS) AF: 0.673 AC: 21717 AN: 32258

South Asian (SAS) AF: 0.367 AC: 15714 AN: 42786

European-Finnish (FIN) AF: 0.388 AC: 16046 AN: 41364

Middle Eastern (MID) AF: 0.372 AC: 830 AN: 2230

European-Non Finnish (NFE) AF: 0.416 AC: 203408 AN: 489504

Other (OTH) AF: 0.437 AC: 14294 AN: 32680

GnomAD4 genome AF: 0.466 AC: 70797 AN: 152070 Hom.: 17011 Cov.: 33 AF XY: 0.465 AC XY: 34576 AN XY: 74352

African (AFR) AF: 0.525 AC: 21771 AN: 41476

American (AMR) AF: 0.539 AC: 8235 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.387 AC: 1343 AN: 3468

East Asian (EAS) AF: 0.699 AC: 3624 AN: 5186

South Asian (SAS) AF: 0.393 AC: 1892 AN: 4820

European-Finnish (FIN) AF: 0.369 AC: 3897 AN: 10560

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

European-Non Finnish (NFE) AF: 0.422 AC: 28674 AN: 67960

Other (OTH) AF: 0.459 AC: 968 AN: 2110

Alfa AF: 0.376 Hom.: 1725

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	-0.85
CADD	Benign	1.8
DANN	Benign	0.51
PhyloP100		-0.062
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: rs361239; hg19: chr3-136701295;