rs992351585
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_173495.3(PTCHD1):c.1582C>A(p.Leu528Ile) variant causes a missense change. The variant allele was found at a frequency of 0.00000273 in 1,097,216 control chromosomes in the GnomAD database, with no homozygous occurrence. There are no hemizygote samples 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. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. L528F) has been classified as Uncertain significance.
Frequency
Consequence
NM_173495.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PTCHD1 | NM_173495.3 | c.1582C>A | p.Leu528Ile | missense_variant | 3/3 | ENST00000379361.5 | |
PTCHD1 | XM_011545449.4 | c.1582C>A | p.Leu528Ile | missense_variant | 4/4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PTCHD1 | ENST00000379361.5 | c.1582C>A | p.Leu528Ile | missense_variant | 3/3 | 1 | NM_173495.3 | P1 | |
PTCHD1 | ENST00000456522.1 | c.*417C>A | 3_prime_UTR_variant | 2/2 | 1 |
Frequencies
GnomAD3 genomes ? Cov.: 23
GnomAD3 exomes AF: 0.00000546 AC: 1AN: 183275Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 67737
GnomAD4 exome AF: 0.00000273 AC: 3AN: 1097216Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 362580
GnomAD4 genome ? Cov.: 23
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at