ClinVar Miner

Submissions for variant NM_000059.3(BRCA2):c.5704G>A (p.Asp1902Asn) (rs4987048)

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Total submissions: 26
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Evidence-based Network for the Interpretation of Germline Mutant Alleles (ENIGMA) RCV000113464 SCV000245034 benign Breast-ovarian cancer, familial 2 2015-01-12 reviewed by expert panel curation Class 1 not pathogenic based on frequency >1% in an outbred sampleset. Frequency 0.01626 (African), derived from 1000 genomes (2012-04-30).
Invitae RCV000167833 SCV000072736 benign Hereditary breast and ovarian cancer syndrome 2020-12-04 criteria provided, single submitter clinical testing
Ambry Genetics RCV000131020 SCV000185947 benign Hereditary cancer-predisposing syndrome 2014-11-19 criteria provided, single submitter clinical testing This alteration is classified as 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.
EGL Genetic Diagnostics, Eurofins Clinical Diagnostics RCV000120340 SCV000202290 benign not specified 2015-05-22 criteria provided, single submitter clinical testing
Counsyl RCV000113464 SCV000220271 benign Breast-ovarian cancer, familial 2 2014-04-28 criteria provided, single submitter literature only
Vantari Genetics RCV000131020 SCV000267018 likely benign Hereditary cancer-predisposing syndrome 2015-12-21 criteria provided, single submitter clinical testing
Michigan Medical Genetics Laboratories,University of Michigan RCV000113464 SCV000267785 benign Breast-ovarian cancer, familial 2 2016-04-21 criteria provided, single submitter clinical testing
Illumina Clinical Services Laboratory,Illumina RCV000113464 SCV000383723 likely benign Breast-ovarian cancer, familial 2 2018-10-29 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). Publications were found based on this search. The evidence from the literature, in combination with allele frequency data from public databases where available, was sufficient to determine this variant is unlikely to cause disease. Therefore, this variant is classified as likely benign.
Illumina Clinical Services Laboratory,Illumina RCV000314320 SCV000383724 likely benign Fanconi anemia, complementation group D1 2018-10-29 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.
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV000167833 SCV000494333 benign Hereditary breast and ovarian cancer syndrome 2014-02-11 criteria provided, single submitter clinical testing
Center for Pediatric Genomic Medicine,Children's Mercy Hospital and Clinics RCV000424920 SCV000511549 likely benign not provided 2016-06-23 criteria provided, single submitter clinical testing Converted during submission to Likely benign.
Baylor Genetics RCV000462033 SCV000541052 benign Familial cancer of breast 2017-02-23 criteria provided, single submitter clinical testing
Fulgent Genetics,Fulgent Genetics RCV000113464 SCV000575756 likely benign Breast-ovarian cancer, familial 2 2016-01-29 criteria provided, single submitter clinical testing
Genetic Services Laboratory, University of Chicago RCV000120340 SCV000593718 benign not specified 2019-02-11 criteria provided, single submitter clinical testing
ARUP Laboratories, Molecular Genetics and Genomics,ARUP Laboratories RCV001283468 SCV000602746 benign none provided 2020-01-28 criteria provided, single submitter clinical testing
Color Health, Inc RCV000131020 SCV000683727 benign Hereditary cancer-predisposing syndrome 2015-03-10 criteria provided, single submitter clinical testing
GeneKor MSA RCV000120340 SCV000693638 benign not specified 2017-11-01 criteria provided, single submitter clinical testing
Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center RCV000113464 SCV000744475 likely benign Breast-ovarian cancer, familial 2 2015-09-21 criteria provided, single submitter clinical testing
PreventionGenetics,PreventionGenetics RCV000120340 SCV000805730 benign not specified 2016-10-03 criteria provided, single submitter clinical testing
ITMI RCV000120340 SCV000084492 not provided not specified 2013-09-19 no assertion provided reference population
Breast Cancer Information Core (BIC) (BRCA2) RCV000113464 SCV000146670 benign Breast-ovarian cancer, familial 2 2002-05-29 no assertion criteria provided clinical testing
Department of Pathology and Laboratory Medicine,Sinai Health System RCV000113464 SCV000591989 benign Breast-ovarian cancer, familial 2 no assertion criteria provided clinical testing The BRCA2 p.Asp1902Asn was identified in 2 of 4284 chromosomes (frequency: 0.0005) from individuals with breast cancer, and was absent in control chromosomes from these studies (Borg 2010, Fackenthal 2005). It is listed in dbSNP (ID#: rs4987048) with a “global minor allele frequency" of 0.004 (1000 Genomes), and in the Exome Variant Server ESP project with a frequency of 0.018 in African American alleles. It is also reported in several populations from the HapMap project, including: HAPMAP-MEX (frequency: 0.031), HAPMAP-LWK (frequency: 0.034), and HapMap-HCB (frequency: 0.038), increasing the likelihood that this is a low frequency benign variant in certain populations of origin. This variant was identified in LOVD, in BIC 87X with no clinical importance, and in UMD 10X as a “neutral” variant where it was reported to co-occur with known pathogenic mutations in BRCA1 and BRCA2 (BRCA2 c.994dup (p.Ile332AsnfsX4), BRCA1 c.3607C>T (p.Arg1203X), BRCA1 c.755_761del (p.Arg252LeufsX44)), further increasing the likelihood that this variant is benign. The p.Asp1902 residue is not conserved in mammals and lower organisms, and computational analyses (PolyPhen2, SIFT, AlignGVGD) do not suggest a high likelihood of impact to the protein, although this information is not predictive enough to rule out pathogenicity. In summary, based on the above information, this variant is classified as benign.
Mayo Clinic Laboratories, Mayo Clinic RCV000424920 SCV000778689 benign not provided 2017-07-24 no assertion criteria provided clinical testing
Foulkes Cancer Genetics LDI, Lady Davis Institute for Medical Research RCV000735573 SCV000863711 uncertain significance Breast and/or ovarian cancer 2002-12-04 no assertion criteria provided clinical testing
Clinical Genetics Laboratory, Department of Pathology,Netherlands Cancer Institute RCV000120340 SCV001905994 benign not specified no assertion criteria provided clinical testing
Human Genetics - Radboudumc,Radboudumc RCV000120340 SCV001957885 benign not specified no assertion criteria provided clinical testing

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