rs58079936
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_ModerateBP6_ModerateBP7BS2
The ENST00000372192.4(PTCH2):c.738C>T(p.Ala246=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000519 in 1,599,702 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. A246A) has been classified as Uncertain significance.
Frequency
Consequence
ENST00000372192.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -9 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PTCH2 | NM_003738.5 | c.738C>T | p.Ala246= | synonymous_variant | 6/22 | ENST00000372192.4 | NP_003729.3 | |
PTCH2 | NM_001166292.2 | c.738C>T | p.Ala246= | synonymous_variant | 6/23 | NP_001159764.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PTCH2 | ENST00000372192.4 | c.738C>T | p.Ala246= | synonymous_variant | 6/22 | 1 | NM_003738.5 | ENSP00000361266 | P2 | |
PTCH2 | ENST00000447098.6 | c.738C>T | p.Ala246= | synonymous_variant | 6/23 | 1 | ENSP00000389703 | A2 |
Frequencies
GnomAD3 genomes AF: 0.0000460 AC: 7AN: 152194Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000443 AC: 11AN: 248434Hom.: 0 AF XY: 0.0000446 AC XY: 6AN XY: 134476
GnomAD4 exome AF: 0.0000525 AC: 76AN: 1447390Hom.: 0 Cov.: 31 AF XY: 0.0000544 AC XY: 39AN XY: 717404
GnomAD4 genome AF: 0.0000460 AC: 7AN: 152312Hom.: 0 Cov.: 31 AF XY: 0.0000671 AC XY: 5AN XY: 74480
ClinVar
Submissions by phenotype
Gorlin syndrome Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Dec 17, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at