rs370936145
Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_ModerateBP6_Very_StrongBP7BS2
The NM_000264.5(PTCH1):c.3195C>T(p.Val1065=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000378 in 1,614,000 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. V1065V) 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 -15 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PTCH1 | NM_000264.5 | c.3195C>T | p.Val1065= | synonymous_variant | 19/24 | ENST00000331920.11 | |
PTCH1 | NM_001083603.3 | c.3192C>T | p.Val1064= | synonymous_variant | 19/24 | ENST00000437951.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PTCH1 | ENST00000331920.11 | c.3195C>T | p.Val1065= | synonymous_variant | 19/24 | 5 | NM_000264.5 | A2 | |
PTCH1 | ENST00000437951.6 | c.3192C>T | p.Val1064= | synonymous_variant | 19/24 | 5 | NM_001083603.3 |
Frequencies
GnomAD3 genomes ? AF: 0.000210 AC: 32AN: 152150Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000637 AC: 16AN: 251090Hom.: 0 AF XY: 0.0000663 AC XY: 9AN XY: 135742
GnomAD4 exome AF: 0.0000198 AC: 29AN: 1461732Hom.: 0 Cov.: 33 AF XY: 0.0000179 AC XY: 13AN XY: 727156
GnomAD4 genome ? AF: 0.000210 AC: 32AN: 152268Hom.: 0 Cov.: 32 AF XY: 0.000282 AC XY: 21AN XY: 74452
ClinVar
Submissions by phenotype
PTCH1-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Dec 06, 2021 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Gorlin syndrome Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 26, 2024 | - - |
Hereditary cancer-predisposing syndrome Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Sep 20, 2018 | 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