GeneBe

6-137004764-TAAAAAA-TAAAAAAAAAA

Variant names:

Variant summary

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

The NM_014432.4(IL20RA):​c.725-8_725-5dupTTTT 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: 7.7e-7 ( 0 hom. )

Consequence

IL20RA
NM_014432.4 splice_region, intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.60

Publications

0 publications found
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]

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ACMG classification

Classification was made for transcript

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
IL20RANM_014432.4 linkc.725-8_725-5dupTTTT 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_725-4insTTTT splice_region_variant, intron_variant Intron 5 of 6 1 NM_014432.4 ENSP00000314976.5 Q9UHF4-1
IL20RAENST00000367748.4 linkc.392-5_392-4insTTTT splice_region_variant, intron_variant Intron 4 of 5 1 ENSP00000356722.1 Q9UHF4-2
IL20RAENST00000541547.5 linkc.578-5_578-4insTTTT splice_region_variant, intron_variant Intron 5 of 6 2 ENSP00000437843.1 Q9UHF4-3
IL20RAENST00000468393.5 linkc.392-5_392-4insTTTT splice_region_variant, intron_variant Intron 4 of 4 4 ENSP00000489177.1 A0A0U1RQU9

Frequencies

GnomAD3 genomes
Cov.:
0
GnomAD4 exome
AF:
7.70e-7
AC:
1
AN:
1298650
Hom.:
0
Cov.:
0
AF XY:
0.00000154
AC XY:
1
AN XY:
647284
show subpopulations
⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.
African (AFR)
AF:
0.0000351
AC:
1
AN:
28516
American (AMR)
AF:
0.00
AC:
0
AN:
28540
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:
72860
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:
0.00
AC:
0
AN:
1007510
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.
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.275
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Exome Het
Variant carriers
0
2
4
6
8
10
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
GnomAD4 genome
Cov.:
0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
PhyloP100
1.6

Splicing

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

Publications

Other links and lift over

dbSNP: rs5880323; hg19: chr6-137325901; API