NM_014432.4:c.725-7_725-5dupTTT

Variant names:

• chr6-137004764-T-TAAA
• rs5880323
• NM_014432.4:c.725-7_725-5dupTTT

Variant summary

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

The NM_014432.4(IL20RA):​c.725-7_725-5dupTTT 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: not found (cov: 0)
  • Exomes 𝑓: 0.0000062 (0 hom.)
• 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 0 ACMG points.

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.725-7_725-5dupTTT		splice_region intron	N/A	NP_055247.4
	IL20RA	NM_001278722.2		c.578-7_578-5dupTTT		splice_region intron	N/A	NP_001265651.2	Q9UHF4-3
	IL20RA	NM_001278723.3		c.392-7_392-5dupTTT		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.725-5_725-4insTTT		splice_region intron	N/A	ENSP00000314976.5	Q9UHF4-1
	IL20RA	ENST00000367748.4	TSL:1	c.392-5_392-4insTTT		splice_region intron	N/A	ENSP00000356722.1	Q9UHF4-2
	IL20RA	ENST00000878901.1		c.728-5_728-4insTTT		splice_region intron	N/A	ENSP00000548960.1

Frequencies

GnomAD3 genomes Cov.: 0

GnomAD4 exome AF: 0.00000616 AC: 8 AN: 1298606 Hom.: 0 Cov.: 0 AF XY: 0.00000772 AC XY: 5 AN XY: 647266

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

African (AFR) AF: 0.000246 AC: 7 AN: 28506

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: 0.00 AC: 0 AN: 72858

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 43608

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

European-Non Finnish (NFE) AF: 9.93e-7 AC: 1 AN: 1007482

Other (OTH) AF: 0.00 AC: 0 AN: 53892

⚠️ 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 Cov.: 0

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs5880323; hg19: chr6-137325901;