| Literature DB >> 32206145 |
Lučka Boltežar1, Gorana Gašljević2, Srdjan Novaković3, Vida Stegel3, Erik Škof1.
Abstract
BACKGROUND: In a patient with a germline BRCA2 pathogenic variant with breast cancer, an adnexal mass can represent either a metachronous primary tumor or a metastasis of the breast cancer. A clear distinction between those two possibilities is crucial since treatments differ substantially and so does survival of the patient. CASEEntities:
Keywords: BRCA2; Breast cancer; Fimbrial part of fallopian tube; Oligometastatic; Receptor conversion
Year: 2020 PMID: 32206145 PMCID: PMC7081695 DOI: 10.1186/s13053-020-00139-w
Source DB: PubMed Journal: Hered Cancer Clin Pract ISSN: 1731-2302 Impact factor: 2.857
Fig. 1Poorly differentiated invasive duct carcinoma of the left breast; H&E, 20x
Fig. 2Metastasis of well differentiated invasive carcinoma in the axillar lymph node; H&E, 20x
Fig. 3Metastasis of poorly differentiated carcinoma into the fimbrial part of left Fallopian tube; H&E, 5x and 40x
Fig. 4Metastasis of poorly differentiated carcinoma into the fimbrial part of left Fallopian tube; H&E, 5x and 40x
Variants detected in three different tumor samples of the same patient. In the table are included only variants reported in whole GnomAD population (ALL) or European or Non-Finish population (NFE) with frequencies < 1%. Variants classified as benign in ClinVar database were removed from the report
| Gene | Variant type | cHGVS | pHGVS | AF (%) in sample 01 | AF (%) in sample 02 | AF (%) in sample 03 | variant status (germline/somatic) | Frequencies in different population in GnomAD database |
|---|---|---|---|---|---|---|---|---|
| BRCA2 | missense_variant | NM_000059.3:c.978C > A | NP_000050.2:p.(Ser326Arg) | 16.96 | 24.69 | 15.98 | confirmed germline varianta | ALL:0.090% - NFE:0.14% |
| FGF5 | 3_prime_UTR_variant | NM_004464.3:c.*1139 T > C | 39.17 | 40.88 | 81.8 | likely germline variantb | ALL:0.89% - NFE:0.82% | |
| FGFR2 | missense_variant | NM_000141.4:c.170C > T | NP_000132.3:p.(Ser57Leu) | 40.64 | 50 | 88.62 | likely germline variantb | ALL:0.45% - NFE:0.31% |
| STK11 | synonymous_variant | NM_000455.4:c.945G > A | NM_000455.4:p.(Pro315=) | 70.77 | 40.5 | 80.77 | confirmed germline varianta | ALL:0.072% - NFE:0.073% |
| BCL6 | splice_region_variant,intron_variant | NM_001706.4:c.1356-3 T > C | p.? | 48.3 | 30.6 | 42.9 | likely germline variantb | ALL:0.24% -NFE:0.18% |
| BRCA2 | splice_acceptor_variant | NM_000059.3:c.8755-1G > A | p.? | 72.3 | 72.6 | 81.2 | confirmed germline varianta | Not known to gnomAD |
| AR | synonymous_variant | NM_000044.3:c.1365 T > G | NM_000044.3:p.(Gly455=) | 13.82 | nd | nd | somatic variantc | Not known to gnomAD |
| RPS6KB1 | synonymous_variant | NM_001272043.1:c.621G > A | NM_001272043.1:p.(Gly207=) | 8.99 | nd | nd | somatic variantc | Not known to gnomAD |
| PDGFRB | missense_variant | NM_002609.3:c.1312G > T | NP_002600.1:p.(Gly438Cys) | nd | 33.2 | nd | somatic variantc | Not known to gnomAD |
| CTNNB1 | synonymous_variant | NM_001904.3:c.765C > A | NM_001904.3:p.(Ala255=) | nd | nd | 77.66 | somatic variantc | Not known to gnomAD |
| ERBB4 | missense_variant | NM_005235.2:c.670C > A | NP_005226.1:p.(Pro224Thr) | nd | nd | 23.68 | somatic variantc | Not known to gnomAD |
| FGF14 | missense_variant | NM_175929.2:c.4G > A | NP_787125.1:p.(Val2Ile) | nd | nd | 37.15 | somatic variantc | ALL:0.00040% |
| NF1 | missense_variant | NM_000267.3:c.7086C > G | NP_000258.1:p.(Asn2362Lys) | nd | nd | 34.25 | somatic variantc | Not known to gnomAD |
| TP53 | missense_variant | NM_000546.5:c.844C > T | NP_000537.3:p.(Arg282Trp) | nd | nd | 73.6 | somatic variantc | ALL:0.00040% - NFE:0.00090% |
| TSC1 | missense_variant | NM_000368.4:c.967C > A | NP_000359.1:p.(Pro323Thr) | nd | nd | 32.35 | somatic variantc | ALL:0.00040% - NFE:0.00090% |
AF allele frequency of nucleotide variant in the sample, nd not detected, cHGVS variant description on coding DNA reference sequence according to Human Genome Variation Society, pHGVS variant description on protein reference sequence according to Human Genome Variation Society
athe variant was confirmed on DNA isolated from patient blood sample, bvariant was classified as likely gemline if the frequency in populations reported in GnomAD database were > 0,005, cvariants not reported in GnomAD or reported in GnomAD with the frequency < 0,005 in different populations