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

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.60
Variant links:
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 0 ACMG points.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
IL20RANM_014432.4 linkc.725-6_725-5dupTT splice_region_variant, intron_variant Intron 5 of 6 ENST00000316649.10 NP_055247.4 Q9UHF4-1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
IL20RAENST00000316649.10 linkc.725-5_725-4insTT splice_region_variant, intron_variant Intron 5 of 6 1 NM_014432.4 ENSP00000314976.5 Q9UHF4-1
IL20RAENST00000367748.4 linkc.392-5_392-4insTT splice_region_variant, intron_variant Intron 4 of 5 1 ENSP00000356722.1 Q9UHF4-2
IL20RAENST00000541547.5 linkc.578-5_578-4insTT splice_region_variant, intron_variant Intron 5 of 6 2 ENSP00000437843.1 Q9UHF4-3
IL20RAENST00000468393.5 linkc.392-5_392-4insTT splice_region_variant, intron_variant Intron 4 of 4 4 ENSP00000489177.1 A0A0U1RQU9

Frequencies

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

Name
Calibrated prediction
Score
Prediction

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs5880323; hg19: chr6-137325901; API