rs142187073
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4BP6_Very_StrongBS2
The NM_003738.5(PTCH2):c.3184G>A(p.Val1062Met) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000119 in 1,614,178 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 (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. V1062G) has been classified as Uncertain significance.
Frequency
Consequence
NM_003738.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -13 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PTCH2 | NM_003738.5 | c.3184G>A | p.Val1062Met | missense_variant | 20/22 | ENST00000372192.4 | |
PTCH2 | NM_001166292.2 | c.3184G>A | p.Val1062Met | missense_variant | 20/23 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PTCH2 | ENST00000372192.4 | c.3184G>A | p.Val1062Met | missense_variant | 20/22 | 1 | NM_003738.5 | P2 | |
PTCH2 | ENST00000447098.6 | c.3184G>A | p.Val1062Met | missense_variant | 20/23 | 1 | A2 |
Frequencies
GnomAD3 genomes AF: 0.000598 AC: 91AN: 152176Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000147 AC: 37AN: 251364Hom.: 0 AF XY: 0.000110 AC XY: 15AN XY: 135894
GnomAD4 exome AF: 0.0000684 AC: 100AN: 1461884Hom.: 0 Cov.: 33 AF XY: 0.0000633 AC XY: 46AN XY: 727246
GnomAD4 genome AF: 0.000604 AC: 92AN: 152294Hom.: 0 Cov.: 32 AF XY: 0.000712 AC XY: 53AN XY: 74472
ClinVar
Submissions by phenotype
Gorlin syndrome Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 16, 2024 | - - |
PTCH2-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Oct 29, 2020 | 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). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at