chrX-23334992-C-T
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_ModerateBP6_ModerateBP7BS2
The NM_173495.3(PTCHD1):c.117C>T(p.Leu39=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000108 in 1,208,418 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 4 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★). Synonymous variant affecting the same amino acid position (i.e. L39L) has been classified as Likely benign.
Frequency
Consequence
NM_173495.3 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -9 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PTCHD1 | NM_173495.3 | c.117C>T | p.Leu39= | synonymous_variant | 1/3 | ENST00000379361.5 | |
PTCHD1 | XM_011545449.4 | c.117C>T | p.Leu39= | synonymous_variant | 2/4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PTCHD1 | ENST00000379361.5 | c.117C>T | p.Leu39= | synonymous_variant | 1/3 | 1 | NM_173495.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00000899 AC: 1AN: 111182Hom.: 0 Cov.: 23 AF XY: 0.00 AC XY: 0AN XY: 33410
GnomAD3 exomes AF: 0.0000337 AC: 6AN: 178227Hom.: 0 AF XY: 0.0000461 AC XY: 3AN XY: 65089
GnomAD4 exome AF: 0.0000109 AC: 12AN: 1097191Hom.: 0 Cov.: 31 AF XY: 0.0000110 AC XY: 4AN XY: 362693
GnomAD4 genome ? AF: 0.00000899 AC: 1AN: 111227Hom.: 0 Cov.: 23 AF XY: 0.00 AC XY: 0AN XY: 33467
ClinVar
Submissions by phenotype
Inborn genetic diseases Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 11, 2019 | 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. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at