rs5880323

Variant names:

• chr6-137004764-TAAAAAA-T
• rs5880323
• NM_014432.4:c.725-10_725-5delTTTTTT

Your query was ambiguous. Multiple possible variants found:

• chr6-137004764-TAAAAAA-T
• chr6-137004764-TAAAAAA-TA
• chr6-137004764-TAAAAAA-TAA
• chr6-137004764-TAAAAAA-TAAA
• chr6-137004764-TAAAAAA-TAAAA
• chr6-137004764-TAAAAAA-TAAAAA
• chr6-137004764-TAAAAAA-TAAAAAAA
• chr6-137004764-TAAAAAA-TAAAAAAAA
• chr6-137004764-TAAAAAA-TAAAAAAAAA
• chr6-137004764-TAAAAAA-TAAAAAAAAAA

Variant summary

Our verdict is Uncertain significance. The variant received 2 ACMG points: 2P and 0B. PM2

The NM_014432.4(IL20RA):​c.725-10_725-5delTTTTTT variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000077 in 1,298,634 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.0 (0 hom., cov: 0)
  • Exomes 𝑓: 7.7e-7 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: IL20RA NM_014432.4 splice_region, intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.60
• Publications: 0 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: Uncertain_significance. The variant received 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	IL20RA	NM_014432.4	MANE Select	c.725-10_725-5delTTTTTT		splice_region intron	N/A	NP_055247.4
	IL20RA	NM_001278722.2		c.578-10_578-5delTTTTTT		splice_region intron	N/A	NP_001265651.2	Q9UHF4-3
	IL20RA	NM_001278723.3		c.392-10_392-5delTTTTTT		splice_region intron	N/A	NP_001265652.2	Q9UHF4-2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	IL20RA	ENST00000316649.10	TSL:1 MANE Select	c.725-10_725-5delTTTTTT		splice_region intron	N/A	ENSP00000314976.5	Q9UHF4-1
	IL20RA	ENST00000367748.4	TSL:1	c.392-10_392-5delTTTTTT		splice_region intron	N/A	ENSP00000356722.1	Q9UHF4-2
	IL20RA	ENST00000878901.1		c.728-10_728-5delTTTTTT		splice_region intron	N/A	ENSP00000548960.1

Frequencies

GnomAD3 genomes AF: 0.00 AC: 0 AN: 146038 Hom.: 0 Cov.: 0

Gnomad AFR AF: 0.00

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

GnomAD4 exome AF: 7.70e-7 AC: 1 AN: 1298634 Hom.: 0 AF XY: 0.00000154 AC XY: 1 AN XY: 647282

⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.

African (AFR) AF: 0.00 AC: 0 AN: 28516

American (AMR) AF: 0.00 AC: 0 AN: 28538

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 22228

East Asian (EAS) AF: 0.00 AC: 0 AN: 36692

South Asian (SAS) AF: 0.0000137 AC: 1 AN: 72860

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 43606

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 4802

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 1007498

Other (OTH) AF: 0.00 AC: 0 AN: 53894

⚠️ The allele balance in gnomAD4 Exomes is highly skewed from 0.5 (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.

GnomAD4 genome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 146038 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 70852

African (AFR) AF: 0.00 AC: 0 AN: 39190

American (AMR) AF: 0.00 AC: 0 AN: 14824

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3440

East Asian (EAS) AF: 0.00 AC: 0 AN: 5086

South Asian (SAS) AF: 0.00 AC: 0 AN: 4652

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 8870

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 312

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 66740

Other (OTH) AF: 0.00 AC: 0 AN: 2018

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		1.6

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs5880323; hg19: chr6-137325901;