chr6-137004764-T-TAA

Variant names:

• chr6-137004764-T-TAA
• rs5880323
• NM_014432.4:c.725-6_725-5dupTT

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 0P and 0B.

The NM_014432.4(IL20RA):​c.725-6_725-5dupTT variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.000034 (0 hom., cov: 0)
  • Exomes 𝑓: 0.00019 (0 hom.)
• Consequence: IL20RA NM_014432.4 splice_region, 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 Uncertain_significance. Variant got 0 ACMG points.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
IL20RA	NM_014432.4	c.725-6_725-5dupTT		splice_region_variant, intron_variant	Intron 5 of 6	ENST00000316649.10	NP_055247.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
IL20RA	ENST00000316649.10	c.725-5_725-4insTT		splice_region_variant, intron_variant	Intron 5 of 6	1	NM_014432.4	ENSP00000314976.5
IL20RA	ENST00000367748.4	c.392-5_392-4insTT		splice_region_variant, intron_variant	Intron 4 of 5	1		ENSP00000356722.1
IL20RA	ENST00000541547.5	c.578-5_578-4insTT		splice_region_variant, intron_variant	Intron 5 of 6	2		ENSP00000437843.1
IL20RA	ENST00000468393.5	c.392-5_392-4insTT		splice_region_variant, intron_variant	Intron 4 of 4	4		ENSP00000489177.1

Frequencies

GnomAD3 genomes AF: 0.0000342 AC: 5 AN: 146040 Hom.: 0 Cov.: 0

Gnomad AFR AF: 0.000128

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00

Gnomad OTH AF: 0.00

GnomAD3 exomes AF: 0.000515 AC: 78 AN: 151602 Hom.: 0 AF XY: 0.000455 AC XY: 38 AN XY: 83602

Gnomad AFR exome AF: 0.00527

Gnomad AMR exome AF: 0.000586

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad SAS exome AF: 0.0000572

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.0000923

Gnomad OTH exome AF: 0.000289

GnomAD4 exome AF: 0.000187 AC: 243 AN: 1298246 Hom.: 0 Cov.: 0 AF XY: 0.000182 AC XY: 118 AN XY: 647076

Gnomad4 AFR exome AF: 0.00674

Gnomad4 AMR exome AF: 0.000456

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.0000275

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.0000159

Gnomad4 OTH exome AF: 0.000371

GnomAD4 genome AF: 0.0000342 AC: 5 AN: 146040 Hom.: 0 Cov.: 0 AF XY: 0.0000423 AC XY: 3 AN XY: 70852

Gnomad4 AFR AF: 0.000128

Gnomad4 AMR AF: 0.00

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.00

Gnomad4 OTH AF: 0.00

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

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;