ClinVar Miner

Variants from ClinGen ENIGMA BRCA1 and BRCA2 Variant Curation Expert Panel, ClinGen with conflicting interpretations

Location: United States  Primary collection method: curation
Minimum review status of the submission from ClinGen ENIGMA BRCA1 and BRCA2 Variant Curation Expert Panel, ClinGen: Collection method of the submission from ClinGen ENIGMA BRCA1 and BRCA2 Variant Curation Expert Panel, ClinGen:
Minimum review status of the other submission: Collection method of the other submission:
Minimum conflict level:
ClinVar version:

If a variant has more than two submissions, it may have multiple conflicts and therefore be counted in more than one conflict column. If this is the case, the "Variants with any kind of conflict" cell will be less than the sum of the conflicted variants cells to its left.

Variants with only 1 submission per condition Variants with at least 2 submissions on the same condition and no conflicts Variants with a synonymous conflict
(e.g. benign vs non-pathogenic)
Variants with a confidence conflict
(e.g. benign vs likely benign)
Variants with a benign or likely benign vs uncertain conflict Variants with a category conflict
(e.g. benign vs affects)
Variants with a clinically significant conflict
(e.g. benign vs pathogenic)
Variants with any conflict
3 11 0 15 13 0 9 26

Significance breakdown #

In the table below, cells that correspond to a term paired with itself represent synonymous conflicts, i.e. variants that have been annotated with different terms that map to the same standard term. To compare the terms that were actually submitted, check the box in the filters section at the top of this page.

All submitters
ClinGen ENIGMA BRCA1 and BRCA2 Variant Curation Expert Panel, ClinGen pathogenic likely pathogenic uncertain significance likely benign
pathogenic 0 5 6 0
likely pathogenic 1 0 1 0
uncertain significance 1 1 0 0
likely benign 1 0 2 0
benign 0 0 11 9

Submitter to submitter summary #

Total submitters: 18
Download table as spreadsheet
Submitter Variants with only 1 submission per condition Variants with at least 2 submissions on the same condition and no conflicts Variants with a synonymous conflict
(e.g. benign vs non-pathogenic)
Variants with a confidence conflict
(e.g. benign vs likely benign)
Variants with a benign or likely benign vs uncertain conflict Variants with a category conflict
(e.g. benign vs affects)
Variants with a clinically significant conflict
(e.g. benign vs pathogenic)
Variants with any conflict
Breast Cancer Information Core (BIC) (BRCA1) 0 7 0 0 7 0 3 10
Sharing Clinical Reports Project (SCRP) 0 16 0 4 1 0 4 9
Breast Cancer Information Core (BIC) (BRCA2) 0 5 0 1 4 0 4 9
Counsyl 0 10 0 4 1 0 1 6
Mendelics 0 2 0 4 1 0 0 5
Illumina Laboratory Services, Illumina 0 0 0 4 1 0 0 5
All of Us Research Program, National Institutes of Health 0 6 0 4 1 0 0 5
Baylor Genetics 0 5 0 2 0 0 0 2
Fulgent Genetics, Fulgent Genetics 0 4 0 2 0 0 0 2
Consortium of Investigators of Modifiers of BRCA1/2 (CIMBA), c/o University of Cambridge 0 12 0 1 0 0 1 2
Genome Diagnostics Laboratory, University Medical Center Utrecht 0 3 0 1 0 0 0 1
Human Genome Sequencing Center Clinical Lab, Baylor College of Medicine 0 4 0 1 0 0 0 1
Pathway Genomics 0 3 0 1 0 0 0 1
Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen 0 7 0 1 0 0 0 1
Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center 0 5 0 1 0 0 0 1
St. Jude Molecular Pathology, St. Jude Children's Research Hospital 0 0 0 1 0 0 0 1
Liquid Biopsy and Cancer Interception Group, Pfizer-University of Granada-Junta de Andalucía Centre for Genomics and Oncological Research 0 0 0 0 1 0 0 1
BRCAlab, Lund University 0 12 0 1 0 0 0 1

All variants with conflicting interpretations #

Total variants: 26
Download table as spreadsheet
HGVS dbSNP gnomAD frequency
NM_007294.4(BRCA1):c.3418A>G (p.Ser1140Gly) rs2227945 0.01054
NM_000059.4(BRCA2):c.7806-40A>G rs9590939 0.00858
NM_000059.4(BRCA2):c.9976A>T (p.Lys3326Ter) rs11571833 0.00597
NM_000059.4(BRCA2):c.8149G>T (p.Ala2717Ser) rs28897747 0.00127
NM_007294.4(BRCA1):c.591C>T (p.Cys197=) rs1799965 0.00117
NM_007294.4(BRCA1):c.2155A>G (p.Lys719Glu) rs80357147 0.00021
NM_007294.4(BRCA1):c.1233T>G (p.Asp411Glu) rs80357024 0.00012
NM_000059.4(BRCA2):c.831T>G (p.Asn277Lys) rs28897705 0.00006
NM_007294.4(BRCA1):c.301+7G>A rs80358113 0.00006
NM_007294.4(BRCA1):c.81-11del rs273902788 0.00004
NM_000059.4(BRCA2):c.663T>G (p.Phe221Leu) rs80358891 0.00003
NM_000059.4(BRCA2):c.9234C>T (p.Val3078=) rs587782428 0.00002
NM_007294.4(BRCA1):c.3082C>T (p.Arg1028Cys) rs80357049 0.00001
NM_000059.4(BRCA2):c.68-7del rs276174878
NM_000059.4(BRCA2):c.7008-5T>C rs397507380
NM_000059.4(BRCA2):c.7879A>T (p.Ile2627Phe) rs80359014
NM_000059.4(BRCA2):c.8168A>C (p.Asp2723Ala) rs41293513
NM_000059.4(BRCA2):c.9227G>T (p.Gly3076Val) rs80359187
NM_000059.4(BRCA2):c.9699_9702del (p.Cys3233fs) rs80359775
NM_000059.4(BRCA2):c.9925G>T (p.Glu3309Ter) rs80359251
NM_007294.4(BRCA1):c.191G>A (p.Cys64Tyr) rs55851803
NM_007294.4(BRCA1):c.305C>G (p.Ala102Gly) rs80357190
NM_007294.4(BRCA1):c.5089T>C (p.Cys1697Arg) rs80356993
NM_007294.4(BRCA1):c.5090G>A (p.Cys1697Tyr) rs397507241
NM_007294.4(BRCA1):c.5194-12G>A rs80358079
NM_007294.4(BRCA1):c.5509T>G (p.Trp1837Gly) rs80356959

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