rs372865581
Variant summary
Our verdict is Benign. Variant got -7 ACMG points: 2P and 9B. PM2BP4_StrongBP7BS2
The NM_003738.5(PTCH2):c.3504C>T(p.Pro1168=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000342 in 1,461,766 control chromosomes in the GnomAD database, with no homozygous occurrence. 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. P1168P) has been classified as Likely benign.
Frequency
Consequence
NM_003738.5 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -7 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PTCH2 | NM_003738.5 | c.3504C>T | p.Pro1168= | synonymous_variant | 22/22 | ENST00000372192.4 | |
PTCH2 | NM_001166292.2 | c.3425+79C>T | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PTCH2 | ENST00000372192.4 | c.3504C>T | p.Pro1168= | synonymous_variant | 22/22 | 1 | NM_003738.5 | P2 | |
PTCH2 | ENST00000447098.6 | c.3425+79C>T | intron_variant | 1 | A2 | ||||
PTCH2 | ENST00000438067.5 | c.186+79C>T | intron_variant | 3 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.00000399 AC: 1AN: 250938Hom.: 0 AF XY: 0.00000737 AC XY: 1AN XY: 135638
GnomAD4 exome AF: 0.00000342 AC: 5AN: 1461766Hom.: 0 Cov.: 32 AF XY: 0.00000413 AC XY: 3AN XY: 727168
GnomAD4 genome Cov.: 32
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at