ClinVar Miner

Submissions for variant NM_024675.3(PALB2):c.3495G>A (p.Ser1165=) (rs45439097)

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Total submissions: 15
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Invitae RCV001082966 SCV000166664 benign Familial cancer of breast 2019-12-31 criteria provided, single submitter clinical testing
GeneDx RCV000212828 SCV000170864 benign not specified 2013-12-25 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 RCV000127303 SCV000212903 likely benign Hereditary cancer-predisposing syndrome 2014-06-15 criteria provided, single submitter clinical testing
PreventionGenetics,PreventionGenetics RCV000212828 SCV000314378 likely benign not specified criteria provided, single submitter clinical testing
Illumina Clinical Services Laboratory,Illumina RCV000384114 SCV000396072 likely benign Fanconi anemia, complementation group N 2017-04-28 criteria provided, single submitter clinical testing This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). No publications were found based on this search. Allele frequency data from public databases allowed determination this variant is unlikely to cause disease. Therefore, this variant is classified as likely benign.
Illumina Clinical Services Laboratory,Illumina RCV000127303 SCV000396073 likely benign Hereditary cancer-predisposing syndrome 2016-06-14 criteria provided, single submitter clinical testing
Quest Diagnostics Nichols Institute San Juan Capistrano RCV000212828 SCV000601787 likely benign not specified 2017-03-22 criteria provided, single submitter clinical testing
Color RCV000127303 SCV000686046 benign Hereditary cancer-predisposing syndrome 2015-04-21 criteria provided, single submitter clinical testing
Integrated Genetics/Laboratory Corporation of America RCV000586081 SCV000699599 benign not provided 2016-04-18 criteria provided, single submitter clinical testing Variant summary: The c.3495G>A variant affects a non-conserved nucleotide, resulting in no amino acid change. One in-silico tool predicts damaging outcome for this variant. 5/5 programs in Alamut predict that this variant does not affect normal splicing, however, it may strengthen a cryptic 5' splicing donor site. ESE finder predicts that this variant may affect multiple ESE sites. However, these predictions are not confirmed by experimental studies. This variant is found in 89/125390 control chromosomes at a frequency of 0.0007098, which is about 5 times of the maximal expected frequency of a pathogenic allele (0.0001563), suggesting this variant is benign. In addition, mutliple clinical laboratories/reputable databases/literatures classified this variant as benign/polymorphism. Taken together, this variant was classified as benign.
PreventionGenetics,PreventionGenetics RCV000586081 SCV000807111 likely benign not provided 2016-01-26 criteria provided, single submitter clinical testing
Quest Diagnostics Nichols Institute San Juan Capistrano RCV000586081 SCV000888377 benign not provided 2018-04-05 criteria provided, single submitter clinical testing
CeGaT Praxis fuer Humangenetik Tuebingen RCV000586081 SCV001150860 uncertain significance not provided 2019-04-01 criteria provided, single submitter clinical testing
ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories RCV000212828 SCV001159009 benign not specified 2019-03-07 criteria provided, single submitter clinical testing
PALB2 database RCV000114630 SCV000148576 likely benign Familial cancer of breast 2012-10-18 no assertion criteria provided literature only
Leiden Open Variation Database RCV000586081 SCV001193417 likely benign not provided 2019-05-13 no assertion criteria provided curation Curators: Marc Tischkowitz, Arleen D. Auerbach. Submitter to LOVD: Marc Tischkowitz.

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