chrX-100296319-T-C
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6BP7
The NM_001184880.2(PCDH19):c.3405A>G(p.Lys1135=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000273 in 1,097,910 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 Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_001184880.2 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PCDH19 | NM_001184880.2 | c.3405A>G | p.Lys1135= | synonymous_variant | 6/6 | ENST00000373034.8 | |
PCDH19 | NM_001105243.2 | c.3264A>G | p.Lys1088= | synonymous_variant | 5/5 | ||
PCDH19 | NM_020766.3 | c.3261A>G | p.Lys1087= | synonymous_variant | 5/5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PCDH19 | ENST00000373034.8 | c.3405A>G | p.Lys1135= | synonymous_variant | 6/6 | 1 | NM_001184880.2 | A1 | |
PCDH19 | ENST00000255531.8 | c.3264A>G | p.Lys1088= | synonymous_variant | 5/5 | 1 | P5 | ||
PCDH19 | ENST00000420881.6 | c.3261A>G | p.Lys1087= | synonymous_variant | 5/5 | 1 | A1 | ||
PCDH19 | ENST00000464981.1 | upstream_gene_variant | 3 |
Frequencies
GnomAD3 genomes ? Cov.: 22
GnomAD4 exome AF: 0.00000273 AC: 3AN: 1097910Hom.: 0 Cov.: 30 AF XY: 0.00000275 AC XY: 1AN XY: 363270
GnomAD4 genome ? Cov.: 22
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Sep 17, 2015 | - - |
Developmental and epileptic encephalopathy, 9 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Nov 10, 2022 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at