chr6-137002258-T-C
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong
The NM_014432.4(IL20RA):c.962A>G(p.Lys321Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000141 in 1,614,002 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_014432.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
IL20RA | NM_014432.4 | c.962A>G | p.Lys321Arg | missense_variant | 7/7 | ENST00000316649.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
IL20RA | ENST00000316649.10 | c.962A>G | p.Lys321Arg | missense_variant | 7/7 | 1 | NM_014432.4 | P1 | |
IL20RA | ENST00000367748.4 | c.629A>G | p.Lys210Arg | missense_variant | 6/6 | 1 | |||
IL20RA | ENST00000541547.5 | c.815A>G | p.Lys272Arg | missense_variant | 7/7 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.000184 AC: 28AN: 152194Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000268 AC: 67AN: 249968Hom.: 0 AF XY: 0.000214 AC XY: 29AN XY: 135398
GnomAD4 exome AF: 0.000136 AC: 199AN: 1461690Hom.: 2 Cov.: 31 AF XY: 0.000127 AC XY: 92AN XY: 727164
GnomAD4 genome ? AF: 0.000184 AC: 28AN: 152312Hom.: 0 Cov.: 32 AF XY: 0.000188 AC XY: 14AN XY: 74482
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jul 06, 2022 | The c.962A>G (p.K321R) alteration is located in exon 7 (coding exon 7) of the IL20RA gene. This alteration results from a A to G substitution at nucleotide position 962, causing the lysine (K) at amino acid position 321 to be replaced by an arginine (R). 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