rs145066065
Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP4_StrongBP6_Very_StrongBS2
The ENST00000372192.4(PTCH2):c.2695+8T>C variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000398 in 1,613,962 control chromosomes in the GnomAD database, including 3 homozygotes. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
ENST00000372192.4 splice_region, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -16 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PTCH2 | NM_003738.5 | c.2695+8T>C | splice_region_variant, intron_variant | ENST00000372192.4 | NP_003729.3 | |||
PTCH2 | NM_001166292.2 | c.2695+8T>C | splice_region_variant, intron_variant | NP_001159764.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PTCH2 | ENST00000372192.4 | c.2695+8T>C | splice_region_variant, intron_variant | 1 | NM_003738.5 | ENSP00000361266 | P2 | |||
PTCH2 | ENST00000447098.6 | c.2695+8T>C | splice_region_variant, intron_variant | 1 | ENSP00000389703 | A2 |
Frequencies
GnomAD3 genomes AF: 0.00191 AC: 291AN: 152174Hom.: 3 Cov.: 32
GnomAD3 exomes AF: 0.000374 AC: 94AN: 251064Hom.: 0 AF XY: 0.000295 AC XY: 40AN XY: 135732
GnomAD4 exome AF: 0.000241 AC: 352AN: 1461670Hom.: 0 Cov.: 34 AF XY: 0.000210 AC XY: 153AN XY: 727142
GnomAD4 genome AF: 0.00191 AC: 291AN: 152292Hom.: 3 Cov.: 32 AF XY: 0.00188 AC XY: 140AN XY: 74478
ClinVar
Submissions by phenotype
Basal cell carcinoma, susceptibility to, 1 Benign:1
Benign, criteria provided, single submitter | clinical testing | KCCC/NGS Laboratory, Kuwait Cancer Control Center | Jul 07, 2023 | - - |
Gorlin syndrome Benign:1
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Nov 27, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at