rs61744561
Variant summary
Our verdict is Benign. Variant got -19 ACMG points: 0P and 19B. BP4_ModerateBP6_Very_StrongBP7BS1BS2
The NM_001184880.2(PCDH19):c.2469G>A(p.Leu823Leu) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00147 in 1,210,055 control chromosomes in the GnomAD database, including 19 homozygotes. There are 445 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 -19 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PCDH19 | NM_001184880.2 | c.2469G>A | p.Leu823Leu | synonymous_variant | Exon 3 of 6 | ENST00000373034.8 | NP_001171809.1 | |
PCDH19 | NM_001105243.2 | c.2328G>A | p.Leu776Leu | synonymous_variant | Exon 2 of 5 | NP_001098713.1 | ||
PCDH19 | NM_020766.3 | c.2328G>A | p.Leu776Leu | synonymous_variant | Exon 2 of 5 | NP_065817.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PCDH19 | ENST00000373034.8 | c.2469G>A | p.Leu823Leu | synonymous_variant | Exon 3 of 6 | 1 | NM_001184880.2 | ENSP00000362125.4 | ||
PCDH19 | ENST00000255531.8 | c.2328G>A | p.Leu776Leu | synonymous_variant | Exon 2 of 5 | 1 | ENSP00000255531.7 | |||
PCDH19 | ENST00000420881.6 | c.2328G>A | p.Leu776Leu | synonymous_variant | Exon 2 of 5 | 1 | ENSP00000400327.2 | |||
PCDH19 | ENST00000636150.1 | c.66-96G>A | intron_variant | Intron 1 of 2 | 5 | ENSP00000490463.1 |
Frequencies
GnomAD3 genomes AF: 0.00747 AC: 836AN: 111985Hom.: 10 Cov.: 23 AF XY: 0.00632 AC XY: 216AN XY: 34161
GnomAD3 exomes AF: 0.00218 AC: 396AN: 181280Hom.: 1 AF XY: 0.00129 AC XY: 87AN XY: 67232
GnomAD4 exome AF: 0.000859 AC: 943AN: 1098021Hom.: 9 Cov.: 31 AF XY: 0.000625 AC XY: 227AN XY: 363395
GnomAD4 genome AF: 0.00749 AC: 839AN: 112034Hom.: 10 Cov.: 23 AF XY: 0.00637 AC XY: 218AN XY: 34220
ClinVar
Submissions by phenotype
not specified Benign:4
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. -
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Developmental and epileptic encephalopathy, 9 Benign:3
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Inborn genetic diseases Benign:1
This alteration is classified as 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. -
not provided Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at