ClinVar Miner

Submissions for variant NM_002834.4(PTPN11):c.990A>C (p.Thr330=) (rs369739920)

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Total submissions: 5
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000033521 SCV000057426 poly Rasopathy criteria provided, single submitter clinical testing Converted during submission to Benign.
Integrated Genetics/Laboratory Corporation of America RCV000587013 SCV000698088 uncertain significance not provided 2017-05-01 criteria provided, single submitter clinical testing Variant summary: The PTPN11 c.990A>C (p.Thr330Thr) 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. 4/5 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 5/121254 control chromosomes at a frequency of 0.0000412, which does not exceed the estimated maximal expected allele frequency of a pathogenic PTPN11 variant (0.0000625). Multiple clinical diagnostic laboratories/reputable databases classified this variant as benign/likely benign, without evidence to independently evaluate. The variant of interest has not, to our knowledge, been reported in affected individuals via publications nor evaluated for functional impact by in vivo/vitro studies. Taken together, this variant is classified as VUS-possibly benign.
Invitae RCV000033521 SCV000776919 likely benign Rasopathy 2017-08-18 criteria provided, single submitter clinical testing
Laboratory for Molecular Medicine,Partners HealthCare Personalized Medicine RCV000220386 SCV000270777 likely benign not specified 2016-01-29 criteria provided, single submitter clinical testing p.Thr330Thr in exon 9 of PTPN11: This variant is not expected to have clinical s ignificance because it does not alter an amino acid residue and is not located w ithin the splice consensus sequence. It has been identified in 2/11546 Latino an d 2/8650 East Asian chromosomes by the Exome Aggregation Consortium (ExAC, http: //exac.broadinstitute.org; dbSNP rs369739920).
PreventionGenetics RCV000220386 SCV000309218 likely benign not specified criteria provided, single submitter clinical testing

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