rs745398684
Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BS1BS2
The NM_001184880.2(PCDH19):āc.2994T>Cā(p.Thr998=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000438 in 1,209,593 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 17 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ā ).
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/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PCDH19 | NM_001184880.2 | c.2994T>C | p.Thr998= | synonymous_variant | 6/6 | ENST00000373034.8 | |
PCDH19 | NM_001105243.2 | c.2853T>C | p.Thr951= | synonymous_variant | 5/5 | ||
PCDH19 | NM_020766.3 | c.2850T>C | p.Thr950= | synonymous_variant | 5/5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PCDH19 | ENST00000373034.8 | c.2994T>C | p.Thr998= | synonymous_variant | 6/6 | 1 | NM_001184880.2 | A1 | |
PCDH19 | ENST00000255531.8 | c.2853T>C | p.Thr951= | synonymous_variant | 5/5 | 1 | P5 | ||
PCDH19 | ENST00000420881.6 | c.2850T>C | p.Thr950= | synonymous_variant | 5/5 | 1 | A1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000269 AC: 3AN: 111437Hom.: 0 Cov.: 22 AF XY: 0.0000298 AC XY: 1AN XY: 33599
GnomAD3 exomes AF: 0.0000275 AC: 5AN: 181582Hom.: 0 AF XY: 0.0000148 AC XY: 1AN XY: 67538
GnomAD4 exome AF: 0.0000455 AC: 50AN: 1098102Hom.: 0 Cov.: 31 AF XY: 0.0000440 AC XY: 16AN XY: 363460
GnomAD4 genome ? AF: 0.0000269 AC: 3AN: 111491Hom.: 0 Cov.: 22 AF XY: 0.0000297 AC XY: 1AN XY: 33663
ClinVar
Submissions by phenotype
Inborn genetic diseases Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 02, 2018 | 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
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Dec 09, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at