chr6-137004764-T-TA

Position:

• chr6-137004764-T-TA

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The NM_014432.4(IL20RA):​c.725-5_725-4insT variant causes a splice region, splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. 1/1 splice prediction tools predict no significant impact on normal splicing. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.046 (498 hom., cov: 0)
  • Exomes 𝑓: 0.0046 (2 hom.)
• Consequence: IL20RA NM_014432.4 splice_region, splice_polypyrimidine_tract, intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.60

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

Verdict is Benign. Variant got -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.159 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
IL20RA	NM_014432.4	c.725-5_725-4insT		splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant		ENST00000316649.10	NP_055247.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
IL20RA	ENST00000316649.10	c.725-5_725-4insT		splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant		1	NM_014432.4	ENSP00000314976	P1
IL20RA	ENST00000367748.4	c.392-5_392-4insT		splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant		1		ENSP00000356722
IL20RA	ENST00000468393.5	c.392-5_392-4insT		splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant		4		ENSP00000489177
IL20RA	ENST00000541547.5	c.578-5_578-4insT		splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant		2		ENSP00000437843

Frequencies

GnomAD3 genomes AF: 0.0457 AC: 6666 AN: 145978 Hom.: 497 Cov.: 0

Gnomad AFR AF: 0.162

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0141

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000215

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00962

Gnomad NFE AF: 0.000764

Gnomad OTH AF: 0.0312

GnomAD3 exomes AF: 0.0126 AC: 1913 AN: 151602 Hom.: 2 AF XY: 0.00949 AC XY: 793 AN XY: 83602

Gnomad AFR exome AF: 0.148

Gnomad AMR exome AF: 0.00801

Gnomad ASJ exome AF: 0.000898

Gnomad EAS exome AF: 0.0000990

Gnomad SAS exome AF: 0.000686

Gnomad FIN exome AF: 0.0000806

Gnomad NFE exome AF: 0.000949

Gnomad OTH exome AF: 0.00463

GnomAD4 exome AF: 0.00456 AC: 5904 AN: 1294468 Hom.: 2 Cov.: 0 AF XY: 0.00416 AC XY: 2682 AN XY: 645320

Gnomad4 AFR exome AF: 0.152

Gnomad4 AMR exome AF: 0.00753

Gnomad4 ASJ exome AF: 0.000676

Gnomad4 EAS exome AF: 0.000164

Gnomad4 SAS exome AF: 0.000881

Gnomad4 FIN exome AF: 0.000138

Gnomad4 NFE exome AF: 0.000814

Gnomad4 OTH exome AF: 0.00906

GnomAD4 genome AF: 0.0458 AC: 6685 AN: 146026 Hom.: 498 Cov.: 0 AF XY: 0.0444 AC XY: 3144 AN XY: 70880

Gnomad4 AFR AF: 0.162

Gnomad4 AMR AF: 0.0141

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.000216

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.000764

Gnomad4 OTH AF: 0.0310

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.040		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: rs5880323; hg19: chr6-137325901;