5-134578727-C-G
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001388185.1(JADE2):āc.1915C>Gā(p.Arg639Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000185 in 1,613,066 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 (ā ).
Frequency
Consequence
NM_001388185.1 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
JADE2 | NM_001388185.1 | c.1915C>G | p.Arg639Gly | missense_variant | 12/12 | ENST00000681547.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
JADE2 | ENST00000681547.2 | c.1915C>G | p.Arg639Gly | missense_variant | 12/12 | NM_001388185.1 | A1 |
Frequencies
GnomAD3 genomes AF: 0.000223 AC: 34AN: 152140Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000339 AC: 83AN: 245148Hom.: 0 AF XY: 0.000285 AC XY: 38AN XY: 133102
GnomAD4 exome AF: 0.000181 AC: 265AN: 1460926Hom.: 0 Cov.: 31 AF XY: 0.000182 AC XY: 132AN XY: 726746
GnomAD4 genome AF: 0.000223 AC: 34AN: 152140Hom.: 0 Cov.: 33 AF XY: 0.000148 AC XY: 11AN XY: 74328
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 06, 2022 | The c.1783C>G (p.R595G) alteration is located in exon 11 (coding exon 10) of the JADE2 gene. This alteration results from a C to G substitution at nucleotide position 1783, causing the arginine (R) at amino acid position 595 to be replaced by a glycine (G). 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