rs11573598
Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP4_StrongBP6_Very_StrongBS2
The NM_003738.5(PTCH2):āc.3363A>Gā(p.Ile1121Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000299 in 1,613,800 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 16/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ā ).
Frequency
Consequence
NM_003738.5 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -16 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PTCH2 | NM_003738.5 | c.3363A>G | p.Ile1121Met | missense_variant | 22/22 | ENST00000372192.4 | |
PTCH2 | NM_001166292.2 | c.3363A>G | p.Ile1121Met | missense_variant | 22/23 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PTCH2 | ENST00000372192.4 | c.3363A>G | p.Ile1121Met | missense_variant | 22/22 | 1 | NM_003738.5 | P2 | |
PTCH2 | ENST00000447098.6 | c.3363A>G | p.Ile1121Met | missense_variant | 22/23 | 1 | A2 | ||
PTCH2 | ENST00000438067.5 | c.126A>G | p.Ile42Met | missense_variant | 3/5 | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.00144 AC: 219AN: 152058Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000358 AC: 90AN: 251210Hom.: 0 AF XY: 0.000287 AC XY: 39AN XY: 135774
GnomAD4 exome AF: 0.000180 AC: 263AN: 1461624Hom.: 0 Cov.: 32 AF XY: 0.000158 AC XY: 115AN XY: 727120
GnomAD4 genome ? AF: 0.00144 AC: 219AN: 152176Hom.: 0 Cov.: 32 AF XY: 0.00144 AC XY: 107AN XY: 74404
ClinVar
Submissions by phenotype
Gorlin syndrome;C0025149:Medulloblastoma;C2751544:Basal cell carcinoma, susceptibility to, 1 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Fulgent Genetics, Fulgent Genetics | Nov 11, 2021 | - - |
Gorlin syndrome Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Dec 21, 2023 | - - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Dec 18, 2020 | In silico analysis supports that this missense variant does not alter protein structure/function; Has not been previously published as pathogenic or benign to our knowledge - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at