rs762888017
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_001184880.2(PCDH19):c.3077C>T(p.Pro1026Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000414 in 1,209,065 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 4 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Synonymous variant affecting the same amino acid position (i.e. P1026P) has been classified as Likely benign.
Frequency
Consequence
NM_001184880.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PCDH19 | NM_001184880.2 | c.3077C>T | p.Pro1026Leu | missense_variant | 6/6 | ENST00000373034.8 | |
PCDH19 | NM_001105243.2 | c.2936C>T | p.Pro979Leu | missense_variant | 5/5 | ||
PCDH19 | NM_020766.3 | c.2933C>T | p.Pro978Leu | missense_variant | 5/5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PCDH19 | ENST00000373034.8 | c.3077C>T | p.Pro1026Leu | missense_variant | 6/6 | 1 | NM_001184880.2 | A1 | |
PCDH19 | ENST00000255531.8 | c.2936C>T | p.Pro979Leu | missense_variant | 5/5 | 1 | P5 | ||
PCDH19 | ENST00000420881.6 | c.2933C>T | p.Pro978Leu | missense_variant | 5/5 | 1 | A1 |
Frequencies
GnomAD3 genomes ? AF: 0.00000900 AC: 1AN: 111124Hom.: 0 Cov.: 22 AF XY: 0.0000300 AC XY: 1AN XY: 33366
GnomAD3 exomes AF: 0.0000110 AC: 2AN: 181398Hom.: 0 AF XY: 0.0000148 AC XY: 1AN XY: 67382
GnomAD4 exome AF: 0.00000364 AC: 4AN: 1097941Hom.: 0 Cov.: 31 AF XY: 0.00000826 AC XY: 3AN XY: 363311
GnomAD4 genome ? AF: 0.00000900 AC: 1AN: 111124Hom.: 0 Cov.: 22 AF XY: 0.0000300 AC XY: 1AN XY: 33366
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Aug 04, 2016 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at