ClinVar Miner

Submissions for variant NM_024675.4(PALB2):c.2365C>T (p.Leu789=)

gnomAD frequency: 0.00099  dbSNP: rs145805054
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Total submissions: 14
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000212810 SCV000211490 benign not specified 2014-06-10 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.
Ambry Genetics RCV000160817 SCV000213606 likely benign Hereditary cancer-predisposing syndrome 2014-12-24 criteria provided, single submitter clinical testing This alteration is classified as likely benign based on a combination of the following: population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity.
Invitae RCV001030300 SCV000252862 benign Familial cancer of breast 2021-12-11 criteria provided, single submitter clinical testing
Quest Diagnostics Nichols Institute San Juan Capistrano RCV000588448 SCV000601757 benign not provided 2019-05-02 criteria provided, single submitter clinical testing
Color Diagnostics, LLC DBA Color Health RCV000160817 SCV000685945 likely benign Hereditary cancer-predisposing syndrome 2015-12-10 criteria provided, single submitter clinical testing
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV000588448 SCV000699563 benign not provided 2016-09-16 criteria provided, single submitter clinical testing Variant summary: The PALB2 c.2365C>T (p.Leu789Leu) variant involves the alteration of a non-conserved nucleotide, resulting in a synonymous change. Mutation taster predicts a benign outcome for this variant. 5/5 splice prediction tools predict no significant impact on normal splicing. This variant was found in 42/121310 control chromosomes, predominantly observed in the African subpopulation at a frequency of 0.0036538 (38/10400). This frequency is about 23 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 African origin. In addition, multiple clinical diagnostic laboratories/reputable databases classified this variant as benign/likely benign. Taken together, this variant is classified as Benign.
Eurofins NTD LLC (GA) RCV000212810 SCV000859962 likely benign not specified 2018-03-21 criteria provided, single submitter clinical testing
CHEO Genetics Diagnostic Laboratory,Children's Hospital of Eastern Ontario RCV001798298 SCV002043594 likely benign Breast and/or ovarian cancer 2020-04-22 criteria provided, single submitter clinical testing
Genetic Services Laboratory,University of Chicago RCV000212810 SCV002070563 likely benign not specified 2018-04-18 criteria provided, single submitter clinical testing
Sema4,Sema4 RCV000160817 SCV002530693 likely benign Hereditary cancer-predisposing syndrome 2021-07-23 criteria provided, single submitter curation
Leiden Open Variation Database RCV001030300 SCV001193216 likely benign Familial cancer of breast 2019-05-13 no assertion criteria provided curation Curators: Marc Tischkowitz, Arleen D. Auerbach. Submitter to LOVD: Marc Tischkowitz.
Genome Diagnostics Laboratory, Amsterdam University Medical Center RCV000588448 SCV001809795 likely benign not provided no assertion criteria provided clinical testing
Clinical Genetics Laboratory, Department of Pathology,Netherlands Cancer Institute RCV000588448 SCV001905901 likely benign not provided no assertion criteria provided clinical testing
Laboratory of Diagnostic Genome Analysis, Leiden University Medical Center (LUMC) RCV000588448 SCV002036091 likely benign not provided no assertion criteria provided clinical testing

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