ENST00000642324.1:c.1533T>C
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1
The ENST00000642324.1(PTCHD3):āc.1533T>Cā(p.Ser511Ser) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.656 in 1,609,400 control chromosomes in the GnomAD database, including 353,605 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Consequence
ENST00000642324.1 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -13 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PTCHD3 | NM_001034842.5 | c.1533T>C | p.Ser511Ser | synonymous_variant | Exon 4 of 4 | NP_001030014.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PTCHD3 | ENST00000642324.1 | c.1533T>C | p.Ser511Ser | synonymous_variant | Exon 4 of 4 | ENSP00000495205.1 |
Frequencies
GnomAD3 genomes AF: 0.622 AC: 94262AN: 151644Hom.: 29785 Cov.: 30
GnomAD3 exomes AF: 0.615 AC: 154404AN: 251090Hom.: 49656 AF XY: 0.631 AC XY: 85592AN XY: 135712
GnomAD4 exome AF: 0.659 AC: 961123AN: 1457638Hom.: 323790 Cov.: 44 AF XY: 0.663 AC XY: 480822AN XY: 725398
GnomAD4 genome AF: 0.622 AC: 94345AN: 151762Hom.: 29815 Cov.: 30 AF XY: 0.623 AC XY: 46252AN XY: 74184
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at