ClinVar Miner

Submissions for variant NM_002834.4(PTPN11):c.854-30T>C (rs144391508)

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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
EGL Genetic Diagnostics,Eurofins Clinical Diagnostics RCV000033511 SCV000058298 benign not specified 2013-03-01 criteria provided, single submitter clinical testing
PreventionGenetics,PreventionGenetics RCV000033511 SCV000309215 benign not specified criteria provided, single submitter clinical testing
Integrated Genetics/Laboratory Corporation of America RCV000033511 SCV000918105 benign not specified 2017-11-28 criteria provided, single submitter clinical testing Variant summary: The PTPN11 c.854-30T>C variant involves the alteration of a non-conserved intronic nucleotide and 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 4526/276876 control chromosomes (320 homozygotes) (gnomAD), predominantly observed in the Latino subpopulation at a frequency of 0.126476 (4349/34386). This frequency is about 2000 times the estimated maximal expected allele frequency of a pathogenic PTPN11 variant (0.0000625), suggesting this is likely a benign polymorphism found primarily in the populations of Latino origin. In addition, multiple clinical diagnostic laboratories/reputable databases classified this variant as benign. Taken together, this variant is classified as benign.
ARUP Laboratories, Molecular Genetics and Genomics,ARUP Laboratories RCV000157029 SCV000206757 benign Noonan syndrome 2014-05-29 no assertion criteria provided clinical testing

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