rs141816797
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_001184880.2(PCDH19):āc.3400A>Cā(p.Asn1134His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00069 in 1,210,055 control chromosomes in the GnomAD database, including 6 homozygotes. There are 280 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 14/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ā ).
Frequency
Consequence
NM_001184880.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PCDH19 | NM_001184880.2 | c.3400A>C | p.Asn1134His | missense_variant | 6/6 | ENST00000373034.8 | |
PCDH19 | NM_001105243.2 | c.3259A>C | p.Asn1087His | missense_variant | 5/5 | ||
PCDH19 | NM_020766.3 | c.3256A>C | p.Asn1086His | missense_variant | 5/5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PCDH19 | ENST00000373034.8 | c.3400A>C | p.Asn1134His | missense_variant | 6/6 | 1 | NM_001184880.2 | A1 | |
PCDH19 | ENST00000255531.8 | c.3259A>C | p.Asn1087His | missense_variant | 5/5 | 1 | P5 | ||
PCDH19 | ENST00000420881.6 | c.3256A>C | p.Asn1086His | missense_variant | 5/5 | 1 | A1 | ||
PCDH19 | ENST00000464981.1 | upstream_gene_variant | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.000572 AC: 64AN: 111972Hom.: 0 Cov.: 23 AF XY: 0.000527 AC XY: 18AN XY: 34128
GnomAD3 exomes AF: 0.00124 AC: 226AN: 181623Hom.: 0 AF XY: 0.00114 AC XY: 77AN XY: 67547
GnomAD4 exome AF: 0.000702 AC: 771AN: 1098028Hom.: 6 Cov.: 30 AF XY: 0.000721 AC XY: 262AN XY: 363388
GnomAD4 genome ? AF: 0.000571 AC: 64AN: 112027Hom.: 0 Cov.: 23 AF XY: 0.000526 AC XY: 18AN XY: 34193
ClinVar
Submissions by phenotype
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | Eurofins Ntd Llc (ga) | Sep 08, 2014 | - - |
Inborn genetic diseases Benign:1
Benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 02, 2018 | 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
Benign, criteria provided, single submitter | clinical testing | GeneDx | Mar 03, 2015 | This variant is associated with the following publications: (PMID: 29924869) - |
Developmental and epileptic encephalopathy, 9 Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 26, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at