chrX-47058415-C-A
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_014735.5(JADE3):c.1810C>A(p.Arg604Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000113 in 1,209,046 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 41 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 12/17 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R604H) has been classified as Uncertain significance.
Frequency
Consequence
NM_014735.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
JADE3 | NM_014735.5 | c.1810C>A | p.Arg604Ser | missense_variant | 11/11 | ENST00000614628.5 | |
JADE3 | NM_001077445.3 | c.1810C>A | p.Arg604Ser | missense_variant | 11/11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
JADE3 | ENST00000614628.5 | c.1810C>A | p.Arg604Ser | missense_variant | 11/11 | 1 | NM_014735.5 | P1 | |
JADE3 | ENST00000611250.4 | c.1810C>A | p.Arg604Ser | missense_variant | 11/11 | 2 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000450 AC: 5AN: 111126Hom.: 0 Cov.: 22 AF XY: 0.0000600 AC XY: 2AN XY: 33326
GnomAD3 exomes AF: 0.0000328 AC: 6AN: 182823Hom.: 0 AF XY: 0.0000148 AC XY: 1AN XY: 67481
GnomAD4 exome AF: 0.000120 AC: 132AN: 1097920Hom.: 0 Cov.: 31 AF XY: 0.000107 AC XY: 39AN XY: 363278
GnomAD4 genome ? AF: 0.0000450 AC: 5AN: 111126Hom.: 0 Cov.: 22 AF XY: 0.0000600 AC XY: 2AN XY: 33326
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | May 26, 2022 | The c.1810C>A (p.R604S) alteration is located in exon 11 (coding exon 10) of the JADE3 gene. This alteration results from a C to A substitution at nucleotide position 1810, causing the arginine (R) at amino acid position 604 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