rs368963363
Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BS1BS2
The NM_001184880.2(PCDH19):c.888C>T(p.Gly296Gly) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00023 in 1,211,236 control chromosomes in the GnomAD database, including 1 homozygotes. There are 150 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 Benign. Variant got -21 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PCDH19 | NM_001184880.2 | c.888C>T | p.Gly296Gly | synonymous_variant | Exon 1 of 6 | ENST00000373034.8 | NP_001171809.1 | |
PCDH19 | NM_001105243.2 | c.888C>T | p.Gly296Gly | synonymous_variant | Exon 1 of 5 | NP_001098713.1 | ||
PCDH19 | NM_020766.3 | c.888C>T | p.Gly296Gly | synonymous_variant | Exon 1 of 5 | NP_065817.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PCDH19 | ENST00000373034.8 | c.888C>T | p.Gly296Gly | synonymous_variant | Exon 1 of 6 | 1 | NM_001184880.2 | ENSP00000362125.4 | ||
PCDH19 | ENST00000255531.8 | c.888C>T | p.Gly296Gly | synonymous_variant | Exon 1 of 5 | 1 | ENSP00000255531.7 | |||
PCDH19 | ENST00000420881.6 | c.888C>T | p.Gly296Gly | synonymous_variant | Exon 1 of 5 | 1 | ENSP00000400327.2 |
Frequencies
GnomAD3 genomes AF: 0.000168 AC: 19AN: 112962Hom.: 0 Cov.: 25 AF XY: 0.000285 AC XY: 10AN XY: 35102
GnomAD3 exomes AF: 0.000529 AC: 96AN: 181633Hom.: 0 AF XY: 0.000726 AC XY: 49AN XY: 67501
GnomAD4 exome AF: 0.000236 AC: 259AN: 1098223Hom.: 1 Cov.: 33 AF XY: 0.000385 AC XY: 140AN XY: 363581
GnomAD4 genome AF: 0.000168 AC: 19AN: 113013Hom.: 0 Cov.: 25 AF XY: 0.000284 AC XY: 10AN XY: 35163
ClinVar
Submissions by phenotype
not specified Benign:1
This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -
Inborn genetic diseases Benign:1
This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. -
Developmental and epileptic encephalopathy, 9 Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at