ClinVar Miner

Submissions for variant NM_024675.3(PALB2):c.1470C>T (p.Pro490=) (rs45612837)

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Total submissions: 13
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Ambry Genetics RCV000127310 SCV000212958 likely benign Hereditary cancer-predisposing syndrome 2014-08-01 criteria provided, single submitter clinical testing
Cancer Genetics Laboratory,Peter MacCallum Cancer Centre RCV000114476 SCV000268043 likely benign Familial cancer of breast 2015-06-01 criteria provided, single submitter case-control
Color RCV000127310 SCV000685883 likely benign Hereditary cancer-predisposing syndrome 2015-04-02 criteria provided, single submitter clinical testing
Counsyl RCV000114476 SCV000786234 likely benign Familial cancer of breast 2018-04-03 criteria provided, single submitter clinical testing
GeneDx RCV000212795 SCV000170871 benign not specified 2014-02-28 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 RCV000276625 SCV000396113 likely benign Fanconi anemia 2016-06-14 criteria provided, single submitter clinical testing
Illumina Clinical Services Laboratory,Illumina RCV000127310 SCV000396114 likely benign Hereditary cancer-predisposing syndrome 2016-06-14 criteria provided, single submitter clinical testing
Integrated Genetics/Laboratory Corporation of America RCV000586468 SCV000699536 benign not provided 2016-12-22 criteria provided, single submitter clinical testing Variant summary: The PALB2 c.1470C>T (p.Pro490Pro) variant involves the alteration of a non-conserved nucleotide, resulting in a synonymous change. One in silico tool predicts a benign outcome for this variant. 5/5 splice prediction tools predict no significant impact on normal splicing. ESE finder predicts that this variant may affect ESE sites. However, these predictions have yet to be confirmed by functional studies. This variant was found in 40/128736 control chromosomes, predominantly observed in the European (Non-Finnish) subpopulation at a frequency of 0.0004196 (28/66726). This frequency is about 3 times the estimated maximal expected allele frequency of a pathogenic PALB2 variant (0.0001563), suggesting this is likely a benign polymorphism found primarily in the populations of European (Non-Finnish) origin. This variant has been reported in multiple affected individuals without strong evidence for causality. In addition, multiple clinical diagnostic laboratories/reputable databases classified this variant as benign/likely benign. Taken together, this variant is classified as benign.
Invitae RCV000114476 SCV000166643 benign Familial cancer of breast 2018-01-09 criteria provided, single submitter clinical testing
PALB2 database RCV000114476 SCV000148422 likely benign Familial cancer of breast 2012-10-18 no assertion criteria provided literature only
Quest Diagnostics Nichols Institute San Juan Capistrano RCV000212795 SCV000601729 likely benign not specified 2017-04-25 criteria provided, single submitter clinical testing
Quest Diagnostics Nichols Institute San Juan Capistrano RCV000586468 SCV000889572 likely benign not provided 2018-04-09 criteria provided, single submitter clinical testing
True Health Diagnostics RCV000127310 SCV000788084 likely benign Hereditary cancer-predisposing syndrome 2017-08-14 no assertion criteria provided clinical testing

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