ClinVar Miner

Submissions for variant NM_000264.4(PTCH1):c.3606C>T (p.Pro1202=) (rs138240178)

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Total submissions: 6
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Ambry Genetics RCV000570819 SCV000674450 benign Hereditary cancer-predisposing syndrome 2016-12-12 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
GeneDx RCV000603526 SCV000725114 benign not specified 2017-11-28 criteria provided, single submitter clinical testing This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease.
Illumina Clinical Services Laboratory,Illumina RCV000205936 SCV000481268 likely benign Gorlin syndrome 2016-06-14 criteria provided, single submitter clinical testing
Illumina Clinical Services Laboratory,Illumina RCV000315816 SCV000481269 likely benign Holoprosencephaly sequence 2016-06-14 criteria provided, single submitter clinical testing
Integrated Genetics/Laboratory Corporation of America RCV000588750 SCV000696380 benign not provided 2016-08-30 criteria provided, single submitter clinical testing Variant summary: The PTCH1 c.3606C>T (p.Pro1202Pro) variant involves the alteration of a non-conserved nucleotide, resulting in a synonymous change. One in silico tool predicts a damaging outcome for this variant. 5/5 splice prediction tools predict no significant impact on normal splicing. However, these predictions have yet to be confirmed by functional studies. This variant was found in 157/26772 control chromosomes (3 homozygotes), predominantly observed in the African subpopulation at a frequency of 0.0475309 (154/3240). This frequency greatly exceeds the estimated maximal expected allele frequency of a pathogenic PTCH1 variant (0.0000171), indicating this is a benign polymorphism found primarily in the populations of African origin. In addition, one clinical diagnostic laboratory/reputable database has classified this variant as benign. The variant of interest has not, to our knowledge, been reported in affected individuals via publications and/or reputable databases/clinical diagnostic laboratories; nor evaluated for functional impact by in vivo/vitro studies. Taken together, this variant is classified as benign.
Invitae RCV000205936 SCV000262280 benign Gorlin syndrome 2018-01-12 criteria provided, single submitter clinical testing

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