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Table 1 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

From: An interesting case of likely BRCA2 related bilateral breast cancer with metastasis in the fimbrial part of fallopian tube

GeneVariant typecHGVSpHGVSAF (%) in sample 01AF (%) in sample 02AF (%) in sample 03variant status (germline/somatic)Frequencies in different population in GnomAD database
BRCA2missense_variantNM_000059.3:c.978C > ANP_000050.2:p.(Ser326Arg)16.9624.6915.98confirmed germline variantaALL:0.090% - NFE:0.14%
FGF53_prime_UTR_variantNM_004464.3:c.*1139 T > C 39.1740.8881.8likely germline variantbALL:0.89% - NFE:0.82%
FGFR2missense_variantNM_000141.4:c.170C > TNP_000132.3:p.(Ser57Leu)40.645088.62likely germline variantbALL:0.45% - NFE:0.31%
STK11synonymous_variantNM_000455.4:c.945G > ANM_000455.4:p.(Pro315=)70.7740.580.77confirmed germline variantaALL:0.072% - NFE:0.073%
BCL6splice_region_variant,intron_variantNM_001706.4:c.1356-3 T > Cp.?48.330.642.9likely germline variantbALL:0.24% -NFE:0.18%
BRCA2splice_acceptor_variantNM_000059.3:c.8755-1G > Ap.?72.372.681.2confirmed germline variantaNot known to gnomAD
ARsynonymous_variantNM_000044.3:c.1365 T > GNM_000044.3:p.(Gly455=)13.82ndndsomatic variantcNot known to gnomAD
RPS6KB1synonymous_variantNM_001272043.1:c.621G > ANM_001272043.1:p.(Gly207=)8.99ndndsomatic variantcNot known to gnomAD
PDGFRBmissense_variantNM_002609.3:c.1312G > TNP_002600.1:p.(Gly438Cys)nd33.2ndsomatic variantcNot known to gnomAD
CTNNB1synonymous_variantNM_001904.3:c.765C > ANM_001904.3:p.(Ala255=)ndnd77.66somatic variantcNot known to gnomAD
ERBB4missense_variantNM_005235.2:c.670C > ANP_005226.1:p.(Pro224Thr)ndnd23.68somatic variantcNot known to gnomAD
FGF14missense_variantNM_175929.2:c.4G > ANP_787125.1:p.(Val2Ile)ndnd37.15somatic variantcALL:0.00040%
NF1missense_variantNM_000267.3:c.7086C > GNP_000258.1:p.(Asn2362Lys)ndnd34.25somatic variantcNot known to gnomAD
TP53missense_variantNM_000546.5:c.844C > TNP_000537.3:p.(Arg282Trp)ndnd73.6somatic variantcALL:0.00040% - NFE:0.00090%
TSC1missense_variantNM_000368.4:c.967C > ANP_000359.1:p.(Pro323Thr)ndnd32.35somatic variantcALL:0.00040% - NFE:0.00090%
  1. 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
  2. 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