chrX-23364549-G-C
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_173495.3(PTCHD1):c.352-15042G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.289 in 109,989 control chromosomes in the GnomAD database, including 3,622 homozygotes. There are 9,429 hemizygotes in GnomAD. 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
NM_173495.3 intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -12 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PTCHD1 | NM_173495.3 | c.352-15042G>C | intron_variant | ENST00000379361.5 | |||
PTCHD1 | XM_011545449.4 | c.352-15042G>C | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PTCHD1 | ENST00000379361.5 | c.352-15042G>C | intron_variant | 1 | NM_173495.3 | P1 | |||
PTCHD1 | ENST00000456522.1 | c.159-27982G>C | intron_variant | 1 |
Frequencies
GnomAD3 genomes AF: 0.289 AC: 31817AN: 109940Hom.: 3624 Cov.: 22 AF XY: 0.292 AC XY: 9406AN XY: 32246
GnomAD4 genome AF: 0.289 AC: 31827AN: 109989Hom.: 3622 Cov.: 22 AF XY: 0.292 AC XY: 9429AN XY: 32305
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at