ClinVar Miner

Submissions for variant NM_000059.3(BRCA2):c.6560C>T (p.Pro2187Leu) (rs56019712)

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Total submissions: 12
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Invitae RCV001081092 SCV000072998 benign Hereditary breast and ovarian cancer syndrome 2020-11-20 criteria provided, single submitter clinical testing
Ambry Genetics RCV000129413 SCV000184183 likely benign Hereditary cancer-predisposing syndrome 2018-01-31 criteria provided, single submitter clinical testing In silico models in agreement (benign);Other data supporting benign classification
GeneDx RCV000589601 SCV000210631 likely benign not provided 2021-06-14 criteria provided, single submitter clinical testing This variant is associated with the following publications: (PMID: 24651015)
Quest Diagnostics Nichols Institute San Juan Capistrano RCV000589601 SCV000600712 likely benign not provided 2019-10-25 criteria provided, single submitter clinical testing
Color Health, Inc RCV000129413 SCV000688987 likely benign Hereditary cancer-predisposing syndrome 2015-04-13 criteria provided, single submitter clinical testing
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV000044985 SCV000694981 likely benign not specified 2020-10-02 criteria provided, single submitter clinical testing Variant summary: BRCA2 c.6560C>T (p.Pro2187Leu) results in a non-conservative amino acid change in the encoded protein sequence. Four of five in-silico tools predict a benign effect of the variant on protein function. The variant allele was found at a frequency of 0.00012 in 246842 control chromosomes, predominantly at a frequency of 0.00083 within the Latino subpopulation in the gnomAD database. The observed variant frequency within Latino control individuals in the gnomAD database is slightly higher than the estimated maximal expected allele frequency for a pathogenic variant in BRCA2 causing Hereditary Breast And Ovarian Cancer Syndrome phenotype (0.00075), suggesting that the variant is a benign polymorphism found primarily in populations of Latino origin. c.6560C>T has been reported in the literature in at least one individual evaluated for Hereditary Breast And Ovarian Cancer Syndrome (Briceno-Balcazar_2017). This report does not provide unequivocal conclusions about association of the variant with Hereditary Breast And Ovarian Cancer Syndrome. To our knowledge, no experimental evidence demonstrating an impact on protein function has been reported. Seven other ClinVar submitters (evaluation after 2014) have cited the variant as likely benign (n=5) and uncertain significance (n=2). Based on the evidence outlined above, the variant was classified as likely benign.
St. Jude Clinical Genomics Lab, St. Jude Children's Research Hospital RCV001081092 SCV000891014 uncertain significance Hereditary breast and ovarian cancer syndrome 2021-08-04 criteria provided, single submitter clinical testing
Illumina Clinical Services Laboratory,Illumina RCV000031634 SCV001267261 uncertain significance Breast-ovarian cancer, familial 2 2018-11-26 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 did not allow this variant to be ruled in or out of causing disease. Therefore, this variant is classified as a variant of unknown significance.
Illumina Clinical Services Laboratory,Illumina RCV001109884 SCV001267262 uncertain significance Fanconi anemia, complementation group D1 2018-11-26 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 did not allow this variant to be ruled in or out of causing disease. Therefore, this variant is classified as a variant of unknown significance.
Baylor Genetics RCV001109884 SCV001522806 uncertain significance Fanconi anemia, complementation group D1 2019-05-29 criteria provided, single submitter clinical testing This variant was determined to be of uncertain significance according to ACMG Guidelines, 2015 [PMID:25741868].
Sharing Clinical Reports Project (SCRP) RCV000031634 SCV000054241 benign Breast-ovarian cancer, familial 2 2011-11-11 no assertion criteria provided clinical testing
Breast Cancer Information Core (BIC) (BRCA2) RCV000031634 SCV000146884 uncertain significance Breast-ovarian cancer, familial 2 2002-05-29 no assertion criteria provided clinical testing

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