rs1338518342
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7
The NM_001184880.2(PCDH19):c.789C>T(p.Ser263=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000413 in 1,211,171 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.789C>T | p.Ser263= | synonymous_variant | 1/6 | ENST00000373034.8 | |
PCDH19 | NM_001105243.2 | c.789C>T | p.Ser263= | synonymous_variant | 1/5 | ||
PCDH19 | NM_020766.3 | c.789C>T | p.Ser263= | synonymous_variant | 1/5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PCDH19 | ENST00000373034.8 | c.789C>T | p.Ser263= | synonymous_variant | 1/6 | 1 | NM_001184880.2 | A1 | |
PCDH19 | ENST00000255531.8 | c.789C>T | p.Ser263= | synonymous_variant | 1/5 | 1 | P5 | ||
PCDH19 | ENST00000420881.6 | c.789C>T | p.Ser263= | synonymous_variant | 1/5 | 1 | A1 |
Frequencies
GnomAD3 genomes ? AF: 0.00000885 AC: 1AN: 113046Hom.: 0 Cov.: 24 AF XY: 0.00 AC XY: 0AN XY: 35184
GnomAD4 exome AF: 0.00000364 AC: 4AN: 1098125Hom.: 0 Cov.: 33 AF XY: 0.00000275 AC XY: 1AN XY: 363481
GnomAD4 genome ? AF: 0.00000885 AC: 1AN: 113046Hom.: 0 Cov.: 24 AF XY: 0.00 AC XY: 0AN XY: 35184
ClinVar
Submissions by phenotype
Developmental and epileptic encephalopathy, 9 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jul 31, 2019 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at