rs201544613
Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BS1BS2
The NM_000264.5(PTCH1):c.1962G>T(p.Thr654=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000292 in 1,613,852 control chromosomes in the GnomAD database, including 2 homozygotes. 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. T654T) 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 -21 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PTCH1 | NM_000264.5 | c.1962G>T | p.Thr654= | synonymous_variant | 14/24 | ENST00000331920.11 | |
PTCH1 | NM_001083603.3 | c.1959G>T | p.Thr653= | synonymous_variant | 14/24 | ENST00000437951.6 | |
LOC100507346 | NR_038982.1 | n.977C>A | non_coding_transcript_exon_variant | 4/4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PTCH1 | ENST00000331920.11 | c.1962G>T | p.Thr654= | synonymous_variant | 14/24 | 5 | NM_000264.5 | A2 | |
PTCH1 | ENST00000437951.6 | c.1959G>T | p.Thr653= | synonymous_variant | 14/24 | 5 | NM_001083603.3 |
Frequencies
GnomAD3 genomes ? AF: 0.000204 AC: 31AN: 151920Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000644 AC: 162AN: 251360Hom.: 1 AF XY: 0.000751 AC XY: 102AN XY: 135838
GnomAD4 exome AF: 0.000302 AC: 441AN: 1461814Hom.: 2 Cov.: 33 AF XY: 0.000400 AC XY: 291AN XY: 727194
GnomAD4 genome ? AF: 0.000204 AC: 31AN: 152038Hom.: 0 Cov.: 32 AF XY: 0.000283 AC XY: 21AN XY: 74306
ClinVar
Submissions by phenotype
Gorlin syndrome Benign:2
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 25, 2024 | - - |
Benign, criteria provided, single submitter | clinical testing | KCCC/NGS Laboratory, Kuwait Cancer Control Center | Jul 07, 2023 | - - |
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | Quest Diagnostics Nichols Institute San Juan Capistrano | May 05, 2021 | - - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Jul 01, 2024 | PTCH1: BP4, BP7, BS1 - |
Hereditary cancer-predisposing syndrome Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | May 09, 2018 | 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. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at