chrX-100296331-T-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.3393A>G(p.Glu1131=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000911 in 1,098,045 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 1 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar 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.3393A>G | p.Glu1131= | synonymous_variant | 6/6 | ENST00000373034.8 | |
PCDH19 | NM_001105243.2 | c.3252A>G | p.Glu1084= | synonymous_variant | 5/5 | ||
PCDH19 | NM_020766.3 | c.3249A>G | p.Glu1083= | synonymous_variant | 5/5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PCDH19 | ENST00000373034.8 | c.3393A>G | p.Glu1131= | synonymous_variant | 6/6 | 1 | NM_001184880.2 | A1 | |
PCDH19 | ENST00000255531.8 | c.3252A>G | p.Glu1084= | synonymous_variant | 5/5 | 1 | P5 | ||
PCDH19 | ENST00000420881.6 | c.3249A>G | p.Glu1083= | synonymous_variant | 5/5 | 1 | A1 | ||
PCDH19 | ENST00000464981.1 | upstream_gene_variant | 3 |
Frequencies
GnomAD3 genomes ? Cov.: 22
GnomAD3 exomes AF: 0.00000551 AC: 1AN: 181631Hom.: 0 AF XY: 0.0000148 AC XY: 1AN XY: 67553
GnomAD4 exome AF: 9.11e-7 AC: 1AN: 1098045Hom.: 0 Cov.: 30 AF XY: 0.00000275 AC XY: 1AN XY: 363407
GnomAD4 genome ? Cov.: 22
ClinVar
Submissions by phenotype
Developmental and epileptic encephalopathy, 9 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Dec 27, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at