chrX-23334992-C-G
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP4_ModerateBP6_ModerateBP7
The NM_173495.3(PTCHD1):c.117C>G(p.Leu39=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000232 in 1,208,418 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 9 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
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PTCHD1 | NM_173495.3 | c.117C>G | p.Leu39= | synonymous_variant | 1/3 | ENST00000379361.5 | |
PTCHD1 | XM_011545449.4 | c.117C>G | p.Leu39= | synonymous_variant | 2/4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PTCHD1 | ENST00000379361.5 | c.117C>G | p.Leu39= | synonymous_variant | 1/3 | 1 | NM_173495.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000180 AC: 2AN: 111182Hom.: 0 Cov.: 23 AF XY: 0.00 AC XY: 0AN XY: 33410
GnomAD3 exomes AF: 0.0000112 AC: 2AN: 178227Hom.: 0 AF XY: 0.0000154 AC XY: 1AN XY: 65089
GnomAD4 exome AF: 0.0000237 AC: 26AN: 1097191Hom.: 0 Cov.: 31 AF XY: 0.0000248 AC XY: 9AN XY: 362693
GnomAD4 genome ? AF: 0.0000180 AC: 2AN: 111227Hom.: 0 Cov.: 23 AF XY: 0.00 AC XY: 0AN XY: 33467
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Oct 17, 2017 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at