chr1-206865938-A-G
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_018724.4(IL20):c.86A>G(p.Asn29Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000684 in 1,461,862 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_018724.4 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
IL20 | NM_018724.4 | c.86A>G | p.Asn29Ser | missense_variant | 2/6 | ENST00000367098.6 | |
IL20 | NM_001385166.1 | c.86A>G | p.Asn29Ser | missense_variant | 3/7 | ||
IL20 | NM_001385167.1 | c.86A>G | p.Asn29Ser | missense_variant | 4/8 | ||
IL20 | NM_001385165.1 | c.86A>G | p.Asn29Ser | missense_variant | 2/5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
IL20 | ENST00000367098.6 | c.86A>G | p.Asn29Ser | missense_variant | 2/6 | 1 | NM_018724.4 | P1 | |
IL20 | ENST00000367096.7 | c.86A>G | p.Asn29Ser | missense_variant | 1/5 | 1 | P1 | ||
IL20 | ENST00000391930.3 | c.86A>G | p.Asn29Ser | missense_variant | 1/4 | 1 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD4 exome AF: 0.00000684 AC: 10AN: 1461862Hom.: 0 Cov.: 32 AF XY: 0.00000550 AC XY: 4AN XY: 727230
GnomAD4 genome ? Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 26, 2023 | The c.86A>G (p.N29S) alteration is located in exon 1 (coding exon 1) of the IL20 gene. This alteration results from a A to G substitution at nucleotide position 86, causing the asparagine (N) at amino acid position 29 to be replaced by a serine (S). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at