rs1317513
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_StrongBP7BS2
The NM_173495.3(PTCHD1):āc.1614C>Gā(p.Thr538=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000298 in 1,209,912 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 7 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. Synonymous variant affecting the same amino acid position (i.e. T538T) has been classified as Uncertain significance.
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.1614C>G | p.Thr538= | synonymous_variant | 3/3 | ENST00000379361.5 | |
PTCHD1 | XM_011545449.4 | c.1614C>G | p.Thr538= | synonymous_variant | 4/4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PTCHD1 | ENST00000379361.5 | c.1614C>G | p.Thr538= | synonymous_variant | 3/3 | 1 | NM_173495.3 | P1 | |
PTCHD1 | ENST00000456522.1 | downstream_gene_variant | 1 |
Frequencies
GnomAD3 genomes AF: 0.000143 AC: 16AN: 112147Hom.: 0 Cov.: 23 AF XY: 0.0000874 AC XY: 3AN XY: 34323
GnomAD3 exomes AF: 0.0000491 AC: 9AN: 183352Hom.: 0 AF XY: 0.0000295 AC XY: 2AN XY: 67810
GnomAD4 exome AF: 0.0000182 AC: 20AN: 1097713Hom.: 0 Cov.: 32 AF XY: 0.0000110 AC XY: 4AN XY: 363081
GnomAD4 genome AF: 0.000143 AC: 16AN: 112199Hom.: 0 Cov.: 23 AF XY: 0.0000872 AC XY: 3AN XY: 34385
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at