chr9-95480453-G-A
Variant summary
Our verdict is Benign. Variant got -17 ACMG points: 0P and 17B. BP4_StrongBP6_Very_StrongBP7BS2
The NM_000264.5(PTCH1):c.882C>T(p.Arg294=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000114 in 1,611,924 control chromosomes in the GnomAD database, with no homozygous occurrence. 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. R294R) has been classified as Likely benign.
Frequency
Consequence
NM_000264.5 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -17 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PTCH1 | NM_000264.5 | c.882C>T | p.Arg294= | synonymous_variant | 6/24 | ENST00000331920.11 | |
PTCH1 | NM_001083603.3 | c.879C>T | p.Arg293= | synonymous_variant | 6/24 | ENST00000437951.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PTCH1 | ENST00000331920.11 | c.882C>T | p.Arg294= | synonymous_variant | 6/24 | 5 | NM_000264.5 | A2 | |
PTCH1 | ENST00000437951.6 | c.879C>T | p.Arg293= | synonymous_variant | 6/24 | 5 | NM_001083603.3 |
Frequencies
GnomAD3 genomes AF: 0.0000734 AC: 11AN: 149938Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.000107 AC: 27AN: 251424Hom.: 0 AF XY: 0.000125 AC XY: 17AN XY: 135878
GnomAD4 exome AF: 0.000118 AC: 173AN: 1461868Hom.: 0 Cov.: 31 AF XY: 0.000106 AC XY: 77AN XY: 727224
GnomAD4 genome AF: 0.0000733 AC: 11AN: 150056Hom.: 0 Cov.: 31 AF XY: 0.0000548 AC XY: 4AN XY: 73026
ClinVar
Submissions by phenotype
not provided Benign:2
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Apr 01, 2023 | PTCH1: BP4, BP7 - |
Benign, criteria provided, single submitter | clinical testing | Quest Diagnostics Nichols Institute San Juan Capistrano | Aug 02, 2022 | - - |
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
Gorlin syndrome Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 25, 2024 | - - |
Hereditary cancer-predisposing syndrome Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Apr 19, 2017 | 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