chr9-95469851-G-A
Variant summary
Our verdict is Benign. Variant got -17 ACMG points: 0P and 17B. BP4_StrongBP6_Very_StrongBP7BS2
The NM_000264.5(PTCH1):c.1809C>T(p.Arg603=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000762 in 1,613,990 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. R603R) has been classified as Likely benign.
Frequency
Consequence
NM_000264.5 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -17 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PTCH1 | NM_000264.5 | c.1809C>T | p.Arg603= | synonymous_variant | 13/24 | ENST00000331920.11 | |
PTCH1 | NM_001083603.3 | c.1806C>T | p.Arg602= | synonymous_variant | 13/24 | ENST00000437951.6 | |
LOC100507346 | NR_038982.1 | n.1789G>A | non_coding_transcript_exon_variant | 4/4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PTCH1 | ENST00000331920.11 | c.1809C>T | p.Arg603= | synonymous_variant | 13/24 | 5 | NM_000264.5 | A2 | |
PTCH1 | ENST00000437951.6 | c.1806C>T | p.Arg602= | synonymous_variant | 13/24 | 5 | NM_001083603.3 |
Frequencies
GnomAD3 genomes AF: 0.000125 AC: 19AN: 152052Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000191 AC: 48AN: 251476Hom.: 0 AF XY: 0.000213 AC XY: 29AN XY: 135914
GnomAD4 exome AF: 0.0000718 AC: 105AN: 1461820Hom.: 0 Cov.: 31 AF XY: 0.0000633 AC XY: 46AN XY: 727228
GnomAD4 genome AF: 0.000118 AC: 18AN: 152170Hom.: 0 Cov.: 32 AF XY: 0.000148 AC XY: 11AN XY: 74388
ClinVar
Submissions by phenotype
Gorlin syndrome Benign:2
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 31, 2024 | - - |
Benign, criteria provided, single submitter | clinical testing | KCCC/NGS Laboratory, Kuwait Cancer Control Center | Jul 07, 2023 | - - |
Hereditary cancer-predisposing syndrome Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 21, 2016 | 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. - |
Gorlin syndrome;C1835820:Holoprosencephaly 7;C2751544:Basal cell carcinoma, susceptibility to, 1 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Fulgent Genetics, Fulgent Genetics | May 31, 2022 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at