6-137020837-T-G

Variant names:

• chr6-137020837-T-G
• rs276477
• NM_014432.4:c.89-3734A>C

Variant summary

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

The NM_014432.4(IL20RA):​c.89-3734A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.82 in 152,176 control chromosomes in the GnomAD database, including 56,545 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 0.82 (56545 hom., cov: 32)
• Consequence: IL20RA NM_014432.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0920
• Publications: 1 publications found

Genes affected

IL20RA (HGNC:6003): (interleukin 20 receptor subunit alpha) This gene encodes a member of the type II cytokine receptor family. The encoded protein is a subunit of the receptor for interleukin 20, a cytokine that may be involved in epidermal function. The interleukin 20 receptor is a heterodimeric complex consisting of the encoded protein and interleukin 20 receptor beta. This gene and interleukin 20 receptor beta are highly expressed in skin, and are upregulated in psoriasis. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jul 2013]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.988 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_014432.4. 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
	IL20RA	NM_014432.4	MANE Select	c.89-3734A>C		intron	N/A	NP_055247.4
	IL20RA	NM_001278722.2		c.-59-3734A>C		intron	N/A	NP_001265651.2
	IL20RA	NM_001278723.3		c.-66-3734A>C		intron	N/A	NP_001265652.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	IL20RA	ENST00000316649.10	TSL:1 MANE Select	c.89-3734A>C		intron	N/A	ENSP00000314976.5
	IL20RA	ENST00000367748.4	TSL:1	c.-66-3734A>C		intron	N/A	ENSP00000356722.1
	IL20RA	ENST00000541547.5	TSL:2	c.-59-3734A>C		intron	N/A	ENSP00000437843.1

Frequencies

GnomAD3 genomes AF: 0.820 AC: 124714 AN: 152058 Hom.: 56538 Cov.: 32

Gnomad AFR AF: 0.393

Gnomad AMI AF: 1.00

Gnomad AMR AF: 0.916

Gnomad ASJ AF: 0.950

Gnomad EAS AF: 1.00

Gnomad SAS AF: 0.995

Gnomad FIN AF: 1.00

Gnomad MID AF: 0.924

Gnomad NFE AF: 0.994

Gnomad OTH AF: 0.845

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

GnomAD4 genome AF: 0.820 AC: 124751 AN: 152176 Hom.: 56545 Cov.: 32 AF XY: 0.826 AC XY: 61422 AN XY: 74400

African (AFR) AF: 0.392 AC: 16265 AN: 41444

American (AMR) AF: 0.916 AC: 14012 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.950 AC: 3297 AN: 3472

East Asian (EAS) AF: 1.00 AC: 5191 AN: 5192

South Asian (SAS) AF: 0.995 AC: 4796 AN: 4818

European-Finnish (FIN) AF: 1.00 AC: 10607 AN: 10610

Middle Eastern (MID) AF: 0.929 AC: 273 AN: 294

European-Non Finnish (NFE) AF: 0.994 AC: 67611 AN: 68032

Other (OTH) AF: 0.847 AC: 1787 AN: 2110

Alfa AF: 0.810 Hom.: 3702

Bravo AF: 0.793

Asia WGS AF: 0.965 AC: 3355 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.084
DANN	Benign	0.36
PhyloP100		0.092
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: rs276477; hg19: chr6-137341974;