chrX-100350665-G-C
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_001184880.2(PCDH19):āc.2656C>Gā(p.Arg886Gly) variant causes a missense change. The variant allele was found at a frequency of 0.00000889 in 112,445 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 1 hemizygotes in GnomAD. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R886Q) has been classified as Uncertain significance.
Frequency
Consequence
NM_001184880.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PCDH19 | NM_001184880.2 | c.2656C>G | p.Arg886Gly | missense_variant | 4/6 | ENST00000373034.8 | |
PCDH19 | NM_001105243.2 | c.2515C>G | p.Arg839Gly | missense_variant | 3/5 | ||
PCDH19 | NM_020766.3 | c.2515C>G | p.Arg839Gly | missense_variant | 3/5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PCDH19 | ENST00000373034.8 | c.2656C>G | p.Arg886Gly | missense_variant | 4/6 | 1 | NM_001184880.2 | A1 | |
PCDH19 | ENST00000255531.8 | c.2515C>G | p.Arg839Gly | missense_variant | 3/5 | 1 | P5 | ||
PCDH19 | ENST00000420881.6 | c.2515C>G | p.Arg839Gly | missense_variant | 3/5 | 1 | A1 | ||
PCDH19 | ENST00000636150.1 | c.157C>G | p.Arg53Gly | missense_variant | 3/3 | 5 |
Frequencies
GnomAD3 genomes AF: 0.00000890 AC: 1AN: 112392Hom.: 0 Cov.: 24 AF XY: 0.0000289 AC XY: 1AN XY: 34576
GnomAD3 exomes AF: 0.00000556 AC: 1AN: 179975Hom.: 0 AF XY: 0.0000152 AC XY: 1AN XY: 65893
GnomAD4 exome Cov.: 25
GnomAD4 genome AF: 0.00000889 AC: 1AN: 112445Hom.: 0 Cov.: 24 AF XY: 0.0000289 AC XY: 1AN XY: 34639
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at