ClinVar Miner

Submissions for variant NM_001083602.2(PTCH1):c.1488C>T (p.Ala496=) (rs2066836)

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Total submissions: 7
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories RCV000589282 SCV000884423 benign not provided 2017-05-18 criteria provided, single submitter clinical testing
Ambry Genetics RCV000492508 SCV000581012 benign Hereditary cancer-predisposing syndrome 2014-12-03 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
Illumina Clinical Services Laboratory,Illumina RCV000342546 SCV000481318 likely benign Gorlin syndrome 2016-06-14 criteria provided, single submitter clinical testing
Illumina Clinical Services Laboratory,Illumina RCV000376238 SCV000481319 likely benign Holoprosencephaly sequence 2016-06-14 criteria provided, single submitter clinical testing
Integrated Genetics/Laboratory Corporation of America RCV000589282 SCV000696372 benign not provided 2016-05-24 criteria provided, single submitter clinical testing Variant summary: The PTCH1 c.1686C>T (p.Ala562Ala) variant causes a synonymous change involving a non-conserved nucleotide with 4/5 splice prediction tools predicting no significant impact on splicing or ESE binding, although these predictions have yet to be functionally assessed. The variant of interest was observed in the large, broad control population, ExAC, with an allele frequency of 20642/118716 (2070 homozygotes, 1/5, frequency: 0.1738772), 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. In addition, the variant has been indicated to co-occur with other pathogenic PTCH1 variants, c.2011_2012dup and c.3050_3051del, in affected individuals via publications. Therefore, taking all available lines of evidence into consideration, the variant of interest is classified as Benign.
Invitae RCV000342546 SCV000622927 benign Gorlin syndrome 2017-07-10 criteria provided, single submitter clinical testing
PreventionGenetics RCV000250191 SCV000303328 benign not specified criteria provided, single submitter clinical testing

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