From: Trans-activation-based risk assessment of BRCA1 BRCT variants with unknown clinical significance
HGVS nucleotide variant | HGVS protein variant | Exon | Type | dbSNP | ClinVar | gnomAD | ESP | HGMD | SIFT | Align GVGD | Mutation taster | Splice prediction | Class |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
c.4956G>A | p.(Met1652Ile) | 16 | Missense | rs1799967 | RCV000112434.6: Benign (ENIGMA) RCV000048709.9: Benign/Likely benign RCV000034756.3: Benign RCV000476093.1: Benign RCV000128916.4: Benign/VUS RCV000120261.7: Benign | ALL: 1.82% AFR: 0.18% AMR: 0.40% EAS: 0.012% SAS: 3.78% NFE: 1.53% FIN: 5.08% OTH: 1.66% | EA: 1.5%AA: 0.2% | CM014325(Disease-causing?) | Tolerated | C0 | Polymorphism (p = 0.964) | None | 1a |
c.4964C>T | p.(Ser1655Phe) | 16 | Missense | rs80357390 | RCV000112436.1: VUS RCV000223580.1: Likely pathogenic |  |  | CM041700(Disease-causing) | Deleterious | C25 | Disease-causing (p = 1) | None | 4b |
c.5075A>C | p.(Asp1692Ala) | 18 | Missense | rs397509222 | RCV000500821.1: VUS RCV000241473.1: VUS |  |  | CM169296(Disease-causing) | Deleterious | C65 | Disease-causing (p = 1) | None | 4 |
c.5095C>T | p.(Arg1699Trp) | 18 | Missense | rs55770810 | RCV000048789.10: Pathogenic RCV000159999.4: Pathogenic RCV000077595.6: Pathogenic (ENIGMA) RCV000191041.1: Pathogenic RCV000457515.1: Pathogenic RCV000239322.2: Pathogenic RCV000131821.4: PathogenicRCV000148390.1: Pathogenic | ALL: 0.0024%EAS: 0.0058% NFE: 0.0018%FIN: 0.0090%OTH: T = 0.11% | EA: 0.01% | CM041706(Disease-causing) | Deleterious | C65 | Disease-causing (p = 1) | None | 5b |
c.5096G>A | p.(Arg1699Gln) | 18 | Missense | rs41293459 | RCV000031217.14: Likely pathogenic RCV000048790.6: Pathogenic/Likely pathogenic RCV000195350.6: Pathogenic/Likely pathogenicRCV000131564.6: Pathogenic/Likely pathogenic | ALL: 0.0024%NFE: 0.0054% |  | CM034007(Disease-causing) | Deleterious | C35 | Disease-causing (p = 1) | None | 4 |
c.5100A>G | p.(Thr1700Thr) | 18 | Synonymous | rs45519437 | RCV000199783.5: Likely benign RCV000428938.2: Benign/Likely benign RCV000494789.2: Likely benign (ENIGMA) RCV000163399.2: Likely benign | ALL: 0.0028%AMR: 0.0060%SAS: 0.0032%NFE: 0.0036% | EA: 0.01% | Â | Â | Â | Â | None | 2 |
c.5116G>A | p.(Gly1706Arg) | 18 | Missense | rs886040864 | RCV000494689.1: Pathogenic RCV000257990.3: Likely pathogenic/VUS |  |  | CM1612904(Disease-causing?) | Deleterious | C65 | Disease-causing (p = 1) | None | 4 |
c.5123C>T | p.(Ala1708Val) | 18 | Missense | rs28897696 | RCV000212194.4: VUS RCV000148393.1: VUS RCV000031221.5: VUS RCV000131166.5: VUS RCV000048803.10: VUS | ALL: 0.0024% AFR: 0.039% | EA: 0.01%AA: 0.05% | CM065004(Disease-causing) | Deleterious | C65 | Disease-causing (p = 1) | None | 3 |
c.5125G>A | p.(Gly1709Arg) | 18 | Missense | rs886038197 | RCV000546570.2: VUS RCV000241163.1: VUS RCV000571176.2: VUS |  |  |  | Deleterious | C15 | Disease-causing (p = 1) | None | 3 |
c.5131A>C | p.(Lys1711Gln) | 18 | Missense |  | RCV000463327.1: VUS |  |  |  | Tolerated | C0 | Disease-causing (p = 0.974) | None | 3 |
c.5252G>A | p.(Arg1751Gln) | 20 | Missense | rs80357442 | RCV000112579.2: Benign (ENIGMA) RCV000257892.6: Benign RCV000162992.3: Benign/Likely benign RCV000168520.7: Benign/Likely benign/VUS RCV000148392.1: VUS | ALL: 0.0041% AMR: 0.0060% NFE: 0.0072% | EA: 0.01% | CM022328(Disease-causing?) | Deleterious | C0 | Disease-causing (p = 0.999) | None | 1a |
c.5309G>T | p.(Gly1770Val) | 21 | Missense |  | RCV000502156.1: Likely pathogenic RCV000477771.1: Likely pathogenic |  |  | CM133533(Disease-causing) | Deleterious | C0 | Disease-causing (p = 1) | None | 4b |
c.5326C>T | p.(Pro1776Ser) | 21 | Missense | rs1800757 | RCV000480229.1: VUS RCV000477350.2: VUS |  | EA: 0.01% |  | Tolerated | C0 | Polymorphism (p = 0.741) | None | 2 |
c.5348T>C | p.(Met1783Thr) | 22 | Missense | rs55808233 | RCV000048954.7: Likely benign RCV000414204.1: VUS RCV000129758.4: Benign/Likely benign RCV000167822.8: Benign/Likely benign/VUS RCV000031240.7: Likely benign | ALL: 0.012%AFR: 0.18%AMR: 0.0060% OTH: 0.018% | AA: 0.18% | CM041721(Disease-causing?) | Deleterious | C45 | Disease-causing (p = 0.999) | None | 2 |
c.5411T>A | p.(Val1804Asp) | 23 | Missense | rs80356920 | RCV000167770.7: Benign RCV000162993.3: Benign/Likely benign RCV000120302.4: Likely benign RCV000148405.1: VUS RCV000112647.4: Benign (ENIGMA) | ALL: 0.010% AMR: 0.048%NFE: 0.0027% | EA: 0.02% | CM044859(Disease-causing?) | Tolerated | C0 | Polymorphism (p = 1) | None | 2a |
c.5477A>T | p.(Glu1826Leu) | 24 | Missense | rs730881499 | RCV000160011.1: VUS | ALL: 0.0033% NFE: 0.0018% FIN: 0.027% |  |  | Tolerated | C0 | Polymorphism (p = 0.763) | None | 2 |
c.5504G>A | p.(Arg1835Gln) | 24 | Missense | rs273902776 | RCV000049023.6: VUS RCV000240743.1: VUS RCV000130437.5: VUS RCV000112685.1: VUS RCV000120265.3: VUS | ALL: 0.0028% AFR: 0.013% EAS: 0.0058% NFE: 0.00090% |  |  | Tolerated | C0 | Disease-causing (p = 0.965) | None | 3 |
c.5513T>G | p.(Val1838Gly) | 24 | Missense | rs80357107 | RCV000241502.1: Likely pathogenic |  |  | CM169297(Disease-causing) | Deleterious | C35 | Disease-causing (p = 1) | None | 4 |