chr1-206866334-A-C
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Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_018724.4(IL20):āc.195A>Cā(p.Leu65Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000682 in 1,613,978 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Genomes: š 0.000079 ( 0 hom., cov: 32)
Exomes š: 0.000067 ( 0 hom. )
Consequence
IL20
NM_018724.4 missense
NM_018724.4 missense
Scores
3
6
9
Clinical Significance
Conservation
PhyloP100: 1.17
Genes affected
IL20 (HGNC:6002): (interleukin 20) The protein encoded by this gene is a cytokine structurally related to interleukin 10 (IL10). This cytokine has been shown to transduce its signal through signal transducer and activator of transcription 3 (STAT3) in keratinocytes. A specific receptor for this cytokine is found to be expressed in skin and upregulated dramatically in psoriatic skin, suggesting a role for this protein in epidermal function and psoriasis. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
IL20 | NM_018724.4 | c.195A>C | p.Leu65Phe | missense_variant | 3/6 | ENST00000367098.6 | |
IL20 | NM_001385166.1 | c.195A>C | p.Leu65Phe | missense_variant | 4/7 | ||
IL20 | NM_001385167.1 | c.195A>C | p.Leu65Phe | missense_variant | 5/8 | ||
IL20 | NM_001385165.1 | c.195A>C | p.Leu65Phe | missense_variant | 3/5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
IL20 | ENST00000367098.6 | c.195A>C | p.Leu65Phe | missense_variant | 3/6 | 1 | NM_018724.4 | P1 | |
IL20 | ENST00000367096.7 | c.195A>C | p.Leu65Phe | missense_variant | 2/5 | 1 | P1 | ||
IL20 | ENST00000391930.3 | c.195A>C | p.Leu65Phe | missense_variant | 2/4 | 1 |
Frequencies
GnomAD3 genomes AF: 0.0000789 AC: 12AN: 152134Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.0000557 AC: 14AN: 251192Hom.: 0 AF XY: 0.0000368 AC XY: 5AN XY: 135742
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GnomAD4 exome AF: 0.0000670 AC: 98AN: 1461844Hom.: 0 Cov.: 32 AF XY: 0.0000729 AC XY: 53AN XY: 727230
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GnomAD4 genome AF: 0.0000789 AC: 12AN: 152134Hom.: 0 Cov.: 32 AF XY: 0.0000673 AC XY: 5AN XY: 74318
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ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 10, 2023 | The c.195A>C (p.L65F) alteration is located in exon 2 (coding exon 2) of the IL20 gene. This alteration results from a A to C substitution at nucleotide position 195, causing the leucine (L) at amino acid position 65 to be replaced by a phenylalanine (F). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Benign
DANN
Uncertain
DEOGEN2
Benign
T;T;.
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Benign
D
M_CAP
Benign
D
MetaRNN
Uncertain
T;T;T
MetaSVM
Benign
T
MutationAssessor
Pathogenic
M;M;M
MutationTaster
Benign
D;D;D
PrimateAI
Benign
T
PROVEAN
Uncertain
D;D;D
REVEL
Uncertain
Sift
Pathogenic
D;D;D
Sift4G
Pathogenic
D;D;D
Polyphen
D;D;.
Vest4
MutPred
Loss of catalytic residue at L65 (P = 0.0675);Loss of catalytic residue at L65 (P = 0.0675);Loss of catalytic residue at L65 (P = 0.0675);
MVP
MPC
ClinPred
D
GERP RS
Varity_R
gMVP
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at