chr9-95508310-TGCCGCC-T
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP6BS2
The NM_000264.5(PTCH1):c.46_51del(p.Gly16_Gly17del) variant causes a inframe deletion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000186 in 1,399,318 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Synonymous variant affecting the same amino acid position (i.e. G16G) has been classified as Likely benign.
Frequency
Consequence
NM_000264.5 inframe_deletion
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PTCH1 | NM_000264.5 | c.46_51del | p.Gly16_Gly17del | inframe_deletion | 1/24 | ENST00000331920.11 | |
PTCH1 | NM_001083603.3 | c.199-1717_199-1712del | intron_variant | ENST00000437951.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PTCH1 | ENST00000331920.11 | c.46_51del | p.Gly16_Gly17del | inframe_deletion | 1/24 | 5 | NM_000264.5 | A2 | |
PTCH1 | ENST00000437951.6 | c.199-1717_199-1712del | intron_variant | 5 | NM_001083603.3 |
Frequencies
GnomAD3 genomes AF: 0.0000133 AC: 2AN: 150744Hom.: 0 Cov.: 32
GnomAD4 exome AF: 0.0000192 AC: 24AN: 1248574Hom.: 0 AF XY: 0.0000148 AC XY: 9AN XY: 608970
GnomAD4 genome AF: 0.0000133 AC: 2AN: 150744Hom.: 0 Cov.: 32 AF XY: 0.0000136 AC XY: 1AN XY: 73570
ClinVar
Submissions by phenotype
Hereditary cancer-predisposing syndrome Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 02, 2022 | The c.46_51delGGCGGC variant (also known as p.G16_G17del) is located in coding exon 1 of the PTCH1 gene. This variant results from an in-frame GGCGGC deletion at nucleotide positions 46 to 51. This results in the in-frame deletion of two glycines at codons 16 and 17. This amino acid region is not well conserved in available vertebrate species. In addition, this alteration is predicted to be neutral by in silico analysis (Choi Y et al. PLoS ONE. 2012; 7(10):e46688). Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear. - |
Gorlin syndrome Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Oct 18, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at