chr1-44822523-G-C
Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2
The NM_003738.5(PTCH2):c.3504C>G(p.Pro1168=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000039 in 1,613,912 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. P1168P) has been classified as Likely benign.
Frequency
Consequence
NM_003738.5 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -11 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PTCH2 | NM_003738.5 | c.3504C>G | p.Pro1168= | synonymous_variant | 22/22 | ENST00000372192.4 | |
PTCH2 | NM_001166292.2 | c.3425+79C>G | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PTCH2 | ENST00000372192.4 | c.3504C>G | p.Pro1168= | synonymous_variant | 22/22 | 1 | NM_003738.5 | P2 | |
PTCH2 | ENST00000447098.6 | c.3425+79C>G | intron_variant | 1 | A2 | ||||
PTCH2 | ENST00000438067.5 | c.186+79C>G | intron_variant | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.00000657 AC: 1AN: 152146Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000359 AC: 9AN: 250938Hom.: 0 AF XY: 0.0000516 AC XY: 7AN XY: 135638
GnomAD4 exome AF: 0.0000424 AC: 62AN: 1461766Hom.: 0 Cov.: 32 AF XY: 0.0000385 AC XY: 28AN XY: 727168
GnomAD4 genome ? AF: 0.00000657 AC: 1AN: 152146Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74328
ClinVar
Submissions by phenotype
Gorlin syndrome Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Dec 09, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at