ClinVar Miner

Submissions for variant NM_001083602.2(PTCH1):c.120C>T (p.Leu40=) (rs1805153)

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Total submissions: 7
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Invitae RCV000589609 SCV000153896 benign not provided 2019-03-06 criteria provided, single submitter clinical testing
PreventionGenetics,PreventionGenetics RCV000253535 SCV000303346 benign not specified criteria provided, single submitter clinical testing
Illumina Clinical Services Laboratory,Illumina RCV000119167 SCV000481350 likely benign Gorlin syndrome 2016-06-14 criteria provided, single submitter clinical testing
Illumina Clinical Services Laboratory,Illumina RCV000265748 SCV000481351 likely benign Holoprosencephaly sequence 2016-06-14 criteria provided, single submitter clinical testing
Ambry Genetics RCV000492253 SCV000581017 benign Hereditary cancer-predisposing syndrome 2016-09-09 criteria provided, single submitter clinical testing Lines of evidence used in support of classification: General population or subpopulation frequency is too high to be a pathogenic mutation based on disease/syndrome prevalence and penetrance
ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories RCV000253535 SCV000604961 benign not specified 2016-06-30 criteria provided, single submitter clinical testing
Integrated Genetics/Laboratory Corporation of America RCV000589609 SCV000696378 benign not provided 2016-05-24 criteria provided, single submitter clinical testing Variant summary: The PTCH1 c.318C>T (p.Leu106Leu) variant causes a synonymous change involving a non-conserved nucleotide with 5/5 splice prediction tools predicting no significant impact on splicing and ESE finder predicting the elimination of an ESE binding site. However, these predictions have yet to be functionally assessed. The variant was observed in the large, broad control population, ExAC, with an allele frequency of 1737/120658 (10 homozygotes, 1/69, frequency: 0.0143961), which significantly exceeds the estimated maximal expected allele frequency for a pathogenic PTCH1 variant of 1/58479 (0.0000171), suggesting this variant is likely a benign polymorphism. The variant has been reported in affected individuals via publications and/or reputable clinical laboratories with a classification of "polymorphism/benign." Therefore, taking all available lines of evidence into consideration, the variant of interest is classified as Benign.

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