rs200347952
Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BS1BS2
The NM_000264.5(PTCH1):c.3240C>T(p.Ala1080Ala) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000558 in 1,614,118 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 (★★).
Frequency
Consequence
NM_000264.5 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -21 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PTCH1 | NM_000264.5 | c.3240C>T | p.Ala1080Ala | synonymous_variant | Exon 19 of 24 | ENST00000331920.11 | NP_000255.2 | |
PTCH1 | NM_001083603.3 | c.3237C>T | p.Ala1079Ala | synonymous_variant | Exon 19 of 24 | ENST00000437951.6 | NP_001077072.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PTCH1 | ENST00000331920.11 | c.3240C>T | p.Ala1080Ala | synonymous_variant | Exon 19 of 24 | 5 | NM_000264.5 | ENSP00000332353.6 | ||
PTCH1 | ENST00000437951.6 | c.3237C>T | p.Ala1079Ala | synonymous_variant | Exon 19 of 24 | 5 | NM_001083603.3 | ENSP00000389744.2 |
Frequencies
GnomAD3 genomes AF: 0.0000328 AC: 5AN: 152222Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000286 AC: 72AN: 251312Hom.: 0 AF XY: 0.000199 AC XY: 27AN XY: 135832
GnomAD4 exome AF: 0.0000581 AC: 85AN: 1461778Hom.: 0 Cov.: 33 AF XY: 0.0000481 AC XY: 35AN XY: 727180
GnomAD4 genome AF: 0.0000328 AC: 5AN: 152340Hom.: 0 Cov.: 32 AF XY: 0.0000403 AC XY: 3AN XY: 74498
ClinVar
Submissions by phenotype
PTCH1-related disorder Benign:1
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
- -
Basal cell nevus syndrome 1 Benign:1
- -
Hereditary cancer-predisposing syndrome Benign:1
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