chr20-44186648-C-G
Variant summary
Our verdict is Likely benign. Variant got -1 ACMG points: 2P and 3B. PM2BP4_ModerateBS1_Supporting
The NM_020433.5(JPH2):āc.58G>Cā(p.Gly20Arg) variant causes a missense change. The variant allele was found at a frequency of 0.0000106 in 1,608,456 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ). Another nucleotide change resulting in same amino acid change has been previously reported as Uncertain significancein ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. G20W) has been classified as Uncertain significance.
Frequency
Consequence
NM_020433.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
JPH2 | NM_020433.5 | c.58G>C | p.Gly20Arg | missense_variant | 1/6 | ENST00000372980.4 | |
JPH2 | NM_175913.4 | c.58G>C | p.Gly20Arg | missense_variant | 1/2 | ||
JPH2 | XM_006723833.5 | c.58G>C | p.Gly20Arg | missense_variant | 1/2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
JPH2 | ENST00000372980.4 | c.58G>C | p.Gly20Arg | missense_variant | 1/6 | 5 | NM_020433.5 | P1 | |
JPH2 | ENST00000342272.3 | c.58G>C | p.Gly20Arg | missense_variant | 1/2 | 1 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152164Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000164 AC: 4AN: 243174Hom.: 0 AF XY: 0.0000151 AC XY: 2AN XY: 132248
GnomAD4 exome AF: 0.0000110 AC: 16AN: 1456292Hom.: 0 Cov.: 38 AF XY: 0.0000110 AC XY: 8AN XY: 724736
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152164Hom.: 0 Cov.: 33 AF XY: 0.0000135 AC XY: 1AN XY: 74332
ClinVar
Submissions by phenotype
Cardiovascular phenotype Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jul 22, 2021 | The p.G20R variant (also known as c.58G>C), located in coding exon 1 of the JPH2 gene, results from a G to C substitution at nucleotide position 58. The glycine at codon 20 is replaced by arginine, an amino acid with dissimilar properties. This amino acid position is conserved. In addition, this alteration is predicted to be tolerated by in silico analysis. Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at