chrX-100406546-G-C
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7
The NM_001184880.2(PCDH19):c.2052C>G(p.Ala684=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★). Synonymous variant affecting the same amino acid position (i.e. A684A) has been classified as Likely benign.
Frequency
Consequence
NM_001184880.2 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PCDH19 | NM_001184880.2 | c.2052C>G | p.Ala684= | synonymous_variant | 1/6 | ENST00000373034.8 | |
PCDH19 | NM_001105243.2 | c.2052C>G | p.Ala684= | synonymous_variant | 1/5 | ||
PCDH19 | NM_020766.3 | c.2052C>G | p.Ala684= | synonymous_variant | 1/5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PCDH19 | ENST00000373034.8 | c.2052C>G | p.Ala684= | synonymous_variant | 1/6 | 1 | NM_001184880.2 | A1 | |
PCDH19 | ENST00000255531.8 | c.2052C>G | p.Ala684= | synonymous_variant | 1/5 | 1 | P5 | ||
PCDH19 | ENST00000420881.6 | c.2052C>G | p.Ala684= | synonymous_variant | 1/5 | 1 | A1 | ||
PCDH19 | ENST00000636150.1 | upstream_gene_variant | 5 |
Frequencies
GnomAD3 genomes Cov.: 23
GnomAD4 exome Cov.: 30
GnomAD4 genome Cov.: 23
ClinVar
Submissions by phenotype
Developmental and epileptic encephalopathy, 9 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Sep 01, 2022 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
No publications associated with this variant yet.