Datasets:
chrom large_stringclasses 5
values | pos int64 10.1M 153M | ref large_stringclasses 4
values | alt large_stringclasses 4
values | label bool 2
classes | subset large_stringclasses 2
values | gene large_stringclasses 8
values | assay large_stringclasses 1
value | mavedb_urn large_stringclasses 8
values | function_score float64 -29.58 4.11 | author_gene large_stringclasses 1
value | author_chromosome int64 17 17 ⌀ | author_position_hg19 int64 41.2M 41.3M ⌀ | author_reference large_stringclasses 4
values | author_alt large_stringclasses 4
values | author_transcript_id large_stringclasses 1
value | author_transcript_position large_stringlengths 1 7 ⌀ | author_transcript_ref large_stringclasses 4
values | author_transcript_alt large_stringclasses 4
values | author_transcript_variant large_stringlengths 6 12 ⌀ | author_aa_pos float64 2 1.86k ⌀ | author_aa_ref large_stringclasses 20
values | author_aa_alt large_stringclasses 20
values | author_protein_variant large_stringlengths 5 8 ⌀ | author_consequence large_stringclasses 11
values | author_function_score_mean float64 -5.65 1.31 ⌀ | author_func_class large_stringclasses 3
values | author_p_nonfunctional float64 0 1 ⌀ | author_experiment large_stringclasses 13
values | author_negative int64 1 250 ⌀ | author_library int64 62 1.5k ⌀ | author_d5_r1 int64 106 15.2k ⌀ | author_d11_r1 int64 1 13.9k ⌀ | author_d5_r2 int64 62 9.44k ⌀ | author_d11_r2 int64 10 18.9k ⌀ | author_neg_freq float64 0 0 ⌀ | author_library_freq float64 0 0 ⌀ | author_d5_freq_r1 float64 0 0.01 ⌀ | author_d11_freq_r1 float64 0 0.01 ⌀ | author_d5_freq_r2 float64 0 0 ⌀ | author_d11_freq_r2 float64 0 0.01 ⌀ | author_d5_lib_ratio_r1 float64 -3.04 3.6 ⌀ | author_loess_fit_r1 float64 -0.88 3.54 ⌀ | author_d11_lib_raw_r1 float64 -10.33 3 ⌀ | author_d11_lib_loess_r1 float64 -10.24 1.46 ⌀ | author_d5_lib_ratio_r2 float64 -2.41 3.23 ⌀ | author_loess_fit_r2 float64 -0.86 3.26 ⌀ | author_d11_lib_raw_r2 float64 -6.5 3.1 ⌀ | author_d11_lib_loess_r2 float64 -6.72 1.78 ⌀ | author_function_score_r1 float64 -6.26 1.5 ⌀ | author_function_score_r2 float64 -5.59 1.26 ⌀ | author_rna_r1 float64 1 17.6k ⌀ | author_rna_r2 float64 1 32.7k ⌀ | author_rna_r1_freq float64 0 0.01 ⌀ | author_rna_r2_freq float64 0 0.01 ⌀ | author_rna_score_1 float64 -6.07 2.38 ⌀ | author_rna_score_2 float64 -5.92 1.76 ⌀ | author_mean_rna_score float64 -5.85 1.12 ⌀ | author_cadd_score float64 0 35 ⌀ | author_phylop_mammalian float64 -4.41 2.87 ⌀ | author_polyphen2 float64 0 1 ⌀ | author_sift float64 0 1 ⌀ | author_agvgd_diff float64 -214.36 354 ⌀ | author_agvgd_class float64 0 65 ⌀ | author_clinvar large_stringclasses 8
values | author_clinvar_simple large_stringclasses 7
values | author_gnomad_af float64 0 0.02 ⌀ | author_bravo_af float64 0 0.01 ⌀ | author_flossies_af float64 0 0.02 ⌀ | author_wt_hap1_function_score_r1 float64 -12.28 19 ⌀ | author_wt_hap1_function_score_r2 float64 -11.29 9.51 ⌀ | author_wt_hap1_function_score_mean float64 -5.8 8.57 ⌀ | consequence large_stringclasses 6
values | consequence_cre large_stringclasses 11
values | exon_closest_pc_gene_id large_stringclasses 9
values | distance_exon_pc int64 0 30 | exon_closest_nc_gene_id large_stringclasses 8
values | distance_exon_nc int64 0 971 | distance_exon int64 0 30 | exon_closest_gene_id large_stringclasses 9
values | consequence_final large_stringclasses 6
values | tss_closest_pc_gene_id large_stringclasses 11
values | distance_tss_pc int64 0 31.9k | tss_closest_nc_gene_id large_stringclasses 11
values | distance_tss_nc int64 0 15.4k | distance_tss int64 0 15.4k | tss_closest_gene_id large_stringclasses 10
values | consequence_group large_stringclasses 2
values | author_accession large_stringlengths 25 28 ⌀ | author_hgvs_nt large_stringlengths 24 30 ⌀ | author_hgvs_splice large_stringclasses 1
value | author_hgvs_pro large_stringclasses 1
value | author_score float64 -29.58 4.11 ⌀ | author_chrom large_stringclasses 3
values | author_pos int64 35.1M 153M ⌀ | author_ref large_stringclasses 4
values | author_exon large_stringclasses 16
values | author_target large_stringclasses 33
values | author_standard_error float64 0 0.12 ⌀ | author_95_ci_upper float64 -0.33 0.3 ⌀ | author_95_ci_lower float64 -0.65 0.09 ⌀ | author_amino_acid_change large_stringlengths 3 5 ⌀ | author_cds_position large_stringlengths 2 6 ⌀ | author_cdna_position large_stringlengths 2 6 ⌀ | author_functional_consequence large_stringclasses 3
values | author_gmm_density_abnormal float64 0 1 ⌀ | author_gmm_density_normal float64 0 1 ⌀ | author_variant_qc_flag large_stringclasses 1
value | author_functional_classification large_stringclasses 4
values | author_z_score_d4_d7 float64 -22.19 3.93 ⌀ | author_z_score_continuous float64 -28.72 4.35 ⌀ | author_bh_fdr_d4_d7 float64 0 1 ⌀ | author_bh_fdr_d4_d14 float64 0 1 ⌀ | author_bh_fdr_continuous float64 0 1 ⌀ | author_processed_adj_lfc_d4_d7 float64 -3.27 0.44 ⌀ | author_processed_adj_lfc_d4_d14 float64 -5.65 0.53 ⌀ | author_processed_adj_lfc_continuous float64 -0.56 0.05 ⌀ | author_two_tailed_p_d4_d7 float64 0 1 ⌀ | author_two_tailed_p_d4_d14 float64 0 1 ⌀ | author_two_tailed_p_continuous float64 0 1 ⌀ | author_se_bind_d4_d7 float64 0.03 0.52 ⌀ | author_se_bind_d4_d14 float64 0.03 0.52 ⌀ | author_se_bind_continuous float64 0 0.08 ⌀ | author_gmm_fast_depleted_z large_stringclasses 611
values | author_gmm_slow_depleted_z large_stringclasses 614
values | author_gmm_uncertainty large_stringclasses 612
values | author_processed_lfc_d4_d7 float64 -0.63 0.6 ⌀ | author_processed_lfc_d4_d10 float64 -1.18 0.41 ⌀ | author_processed_lfc_d4_d14 float64 -2.24 0.57 ⌀ | author_processed_lfc_d4_d21 float64 -3.7 0.56 ⌀ | author_processed_lfc_continuous float64 -0.22 0.03 ⌀ | author_se_bind_d4_d10 float64 0.03 0.52 ⌀ | author_se_bind_d4_d21 float64 0.03 0.48 ⌀ | author_processed_z_d4_d7 float64 -5.72 3.4 ⌀ | author_processed_z_d4_d10 float64 -13.34 4.17 ⌀ | author_processed_z_d4_d14 float64 -23.13 6.21 ⌀ | author_processed_z_d4_d21 float64 -38.62 7.58 ⌀ | author_processed_z_continuous float64 -32.03 9.16 ⌀ | author_processed_bh_fdr_d4_d7 float64 0 1 ⌀ | author_processed_bh_fdr_d4_d10 float64 0 1 ⌀ | author_processed_bh_fdr_d4_d14 float64 0 1 ⌀ | author_processed_bh_fdr_d4_d21 float64 0 1 ⌀ | author_processed_bh_fdr_continuous float64 0 1 ⌀ | author_confidence_of_functionally_abnormal_variant_prediction large_stringclasses 3
values | author_sge_prediction_of_variant_function_in_ndd_context large_stringclasses 2
values | author_protein_position large_stringclasses 660
values | author_score_no_dab large_stringlengths 2 12 ⌀ | author_score_hap1_hif1a_ko large_stringclasses 456
values | author_rna_score_d6 large_stringclasses 889
values | author_rna_score_d20 large_stringclasses 889
values | assay_phenotypic_assay_method large_stringclasses 3
values | assay_delivery_method large_stringclasses 1
value | assay_endogenous_locus_library_method_mechanism large_stringclasses 1
value | assay_endogenous_locus_library_method_system large_stringclasses 1
value | assay_phenotypic_assay_dimensionality large_stringclasses 1
value | assay_phenotypic_assay_mechanism large_stringclasses 1
value | assay_phenotypic_assay_model_system large_stringclasses 1
value | assay_phenotypic_assay_profiling_strategy large_stringclasses 1
value | assay_phenotypic_assay_sequencing_read_type large_stringclasses 1
value | assay_variant_library_creation_method large_stringclasses 1
value | assay_molecular_mechanism_assessed large_stringclasses 1
value | author_class_harmonized large_stringclasses 3
values | calibrated_class large_stringclasses 2
values | calibration_scheme large_stringclasses 3
values | acmg_strength large_stringclasses 5
values | function_direction int8 -1 1 | function_score_aligned float64 -29.58 4.11 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
17 | 43,045,705 | T | C | false | missense_variant | BRCA1 | sge | urn:mavedb:00000097-0-2 | 0.021941 | BRCA1 | 17 | 41,197,722 | T | C | NM_007294.3 | 5565 | A | G | c.5565A>G | 1,855 | I | M | p.I1855M | Missense | 0.021941 | FUNC | 0 | X23 | 2 | 436 | 2,908 | 3,037 | 2,760 | 2,334 | 0.000012 | 0.001169 | 0.000833 | 0.001113 | 0.000632 | 0.000855 | -0.201028 | -0.211658 | -0.012648 | 0.19901 | -0.581616 | -0.345219 | -0.500256 | -0.155037 | 0.174501 | -0.13062 | 1,406 | 666 | 0.001194 | 0.000399 | 0.404663 | -1.054867 | -0.289526 | 23.5 | -0.494 | 0.94 | 0 | 96.19 | 0 | absent | absent | 0 | 0 | 0 | -1.499307 | -0.006078 | -0.752692 | missense_variant | missense_variant | ENSG00000012048 | 0 | ENSG00000012048 | 0 | 0 | ENSG00000012048 | missense_variant | ENSG00000108830 | 20,473 | ENSG00000012048 | 2,767 | 2,767 | ENSG00000012048 | missense_variant | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | Cell fitness | Chemical-based transfection | Nuclease | SpCas9 | Single-dimensional data | Loss of function | Immortalized human cells | Direct sequencing | Single-segment (short read) | Endogenous locus library method | Molecular function | normal | normal | ExCALIBR calibration | STRONG | 1 | 0.021941 |
17 | 43,045,706 | A | C | false | missense_variant | BRCA1 | sge | urn:mavedb:00000097-0-2 | -0.464328 | BRCA1 | 17 | 41,197,723 | A | C | NM_007294.3 | 5564 | T | G | c.5564T>G | 1,855 | I | R | p.I1855R | Missense | -0.464328 | FUNC | 0.000174 | X23 | 2 | 505 | 3,132 | 2,701 | 3,878 | 1,530 | 0.000012 | 0.001354 | 0.000898 | 0.00099 | 0.000887 | 0.00056 | -0.305926 | -0.233129 | -0.393756 | -0.160627 | -0.302926 | -0.386404 | -1.321484 | -0.93508 | -0.140845 | -0.787812 | 2,449 | 1,310 | 0.00208 | 0.000785 | 1.098202 | -0.569539 | 0.343402 | 26.2 | 2.232 | 0.969 | 0 | 35.57 | 0 | absent | absent | 0 | 0 | 0 | null | null | null | missense_variant | missense_variant | ENSG00000012048 | 0 | ENSG00000012048 | 0 | 0 | ENSG00000012048 | missense_variant | ENSG00000108830 | 20,474 | ENSG00000012048 | 2,766 | 2,766 | ENSG00000012048 | missense_variant | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | Cell fitness | Chemical-based transfection | Nuclease | SpCas9 | Single-dimensional data | Loss of function | Immortalized human cells | Direct sequencing | Single-segment (short read) | Endogenous locus library method | Molecular function | normal | normal | ExCALIBR calibration | STRONG | 1 | -0.464328 |
17 | 43,045,706 | A | G | false | missense_variant | BRCA1 | sge | urn:mavedb:00000097-0-2 | -0.291519 | BRCA1 | 17 | 41,197,723 | A | G | NM_007294.3 | 5564 | T | C | c.5564T>C | 1,855 | I | T | p.I1855T | Missense | -0.291519 | FUNC | 0.000017 | X23 | 1 | 518 | 2,905 | 2,124 | 4,174 | 2,750 | 0.000006 | 0.001388 | 0.000832 | 0.000778 | 0.000955 | 0.001007 | -0.451141 | -0.233129 | -0.777135 | -0.544006 | -0.233477 | -0.386404 | -0.512253 | -0.125849 | -0.477009 | -0.106029 | 1,146 | 3,101 | 0.000973 | 0.001859 | 0.111163 | 0.56751 | 0.30377 | 27.2 | 2.232 | 0.882 | 0 | 46.77 | 0 | Uncertain significance | Uncertain significance | 0 | 0 | 0 | 0.125479 | 0.521103 | 0.323291 | missense_variant | missense_variant | ENSG00000012048 | 0 | ENSG00000012048 | 0 | 0 | ENSG00000012048 | missense_variant | ENSG00000108830 | 20,474 | ENSG00000012048 | 2,766 | 2,766 | ENSG00000012048 | missense_variant | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | Cell fitness | Chemical-based transfection | Nuclease | SpCas9 | Single-dimensional data | Loss of function | Immortalized human cells | Direct sequencing | Single-segment (short read) | Endogenous locus library method | Molecular function | normal | normal | ExCALIBR calibration | STRONG | 1 | -0.291519 |
17 | 43,045,707 | T | A | false | missense_variant | BRCA1 | sge | urn:mavedb:00000097-0-2 | -0.218034 | BRCA1 | 17 | 41,197,724 | T | A | NM_007294.3 | 5563 | A | T | c.5563A>T | 1,855 | I | L | p.I1855L | Missense | -0.218034 | FUNC | 0.000007 | X23 | 3 | 477 | 3,170 | 2,450 | 3,489 | 2,186 | 0.000018 | 0.001279 | 0.000908 | 0.000898 | 0.000798 | 0.000801 | -0.206233 | -0.250194 | -0.452174 | -0.20198 | -0.373131 | -0.417057 | -0.724428 | -0.307371 | -0.177105 | -0.258962 | 652 | 1,111 | 0.000554 | 0.000666 | -0.828445 | -0.654748 | -0.805836 | 23.6 | -0.129 | 0.403 | 0.01 | 96.19 | 0 | absent | absent | 0 | 0 | 0 | -0.068912 | -0.552025 | -0.310468 | missense_variant | missense_variant | ENSG00000012048 | 0 | ENSG00000012048 | 0 | 0 | ENSG00000012048 | missense_variant | ENSG00000108830 | 20,475 | ENSG00000012048 | 2,765 | 2,765 | ENSG00000012048 | missense_variant | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | Cell fitness | Chemical-based transfection | Nuclease | SpCas9 | Single-dimensional data | Loss of function | Immortalized human cells | Direct sequencing | Single-segment (short read) | Endogenous locus library method | Molecular function | normal | normal | ExCALIBR calibration | STRONG | 1 | -0.218034 |
17 | 43,045,707 | T | C | false | missense_variant | BRCA1 | sge | urn:mavedb:00000097-0-2 | 0.046278 | BRCA1 | 17 | 41,197,724 | T | C | NM_007294.3 | 5563 | A | G | c.5563A>G | 1,855 | I | V | p.I1855V | Missense | 0.046278 | FUNC | 0 | X23 | 79 | 432 | 2,559 | 3,091 | 3,343 | 2,166 | 0.000465 | 0.001158 | 0.000733 | 0.001133 | 0.000765 | 0.000793 | -0.372178 | -0.250194 | 0.026076 | 0.27627 | -0.291844 | -0.417057 | -0.59473 | -0.177674 | 0.242246 | -0.149691 | 973 | 566 | 0.000826 | 0.000339 | 0.058025 | -1.566063 | -0.684578 | 6.192 | -0.129 | 0.03 | 0.65 | 96.19 | 0 | absent | absent | 0 | 0 | 0 | 0.854759 | -0.548796 | 0.152981 | missense_variant | missense_variant | ENSG00000012048 | 0 | ENSG00000012048 | 0 | 0 | ENSG00000012048 | missense_variant | ENSG00000108830 | 20,475 | ENSG00000012048 | 2,765 | 2,765 | ENSG00000012048 | missense_variant | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | Cell fitness | Chemical-based transfection | Nuclease | SpCas9 | Single-dimensional data | Loss of function | Immortalized human cells | Direct sequencing | Single-segment (short read) | Endogenous locus library method | Molecular function | normal | normal | ExCALIBR calibration | STRONG | 1 | 0.046278 |
17 | 43,045,707 | T | G | false | missense_variant | BRCA1 | sge | urn:mavedb:00000097-0-2 | 0.233297 | BRCA1 | 17 | 41,197,724 | T | G | NM_007294.3 | 5563 | A | C | c.5563A>C | 1,855 | I | L | p.I1855L | Missense | 0.233297 | FUNC | 0 | X23 | 1 | 473 | 3,700 | 4,090 | 4,637 | 2,649 | 0.000006 | 0.001268 | 0.00106 | 0.001499 | 0.001061 | 0.00097 | 0.028958 | -0.250194 | 0.299294 | 0.549489 | 0.049396 | -0.417057 | -0.435125 | -0.018068 | 0.481817 | -0.015222 | 2,130 | 2,648 | 0.001809 | 0.001588 | 0.656422 | 0.187918 | 0.343346 | 23.6 | -0.129 | 0.403 | 0.01 | 96.19 | 0 | absent | absent | 0 | 0 | 0 | 0.370209 | -0.460596 | -0.045193 | missense_variant | missense_variant | ENSG00000012048 | 0 | ENSG00000012048 | 0 | 0 | ENSG00000012048 | missense_variant | ENSG00000108830 | 20,475 | ENSG00000012048 | 2,765 | 2,765 | ENSG00000012048 | missense_variant | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | Cell fitness | Chemical-based transfection | Nuclease | SpCas9 | Single-dimensional data | Loss of function | Immortalized human cells | Direct sequencing | Single-segment (short read) | Endogenous locus library method | Molecular function | normal | normal | ExCALIBR calibration | STRONG | 1 | 0.233297 |
17 | 43,045,709 | A | C | false | missense_variant | BRCA1 | sge | urn:mavedb:00000097-0-2 | 0.312452 | BRCA1 | 17 | 41,197,726 | A | C | NM_007294.3 | 5561 | T | G | c.5561T>G | 1,854 | L | R | p.L1854R | Missense | 0.312452 | FUNC | 0 | X23 | 4 | 406 | 2,566 | 2,934 | 3,305 | 3,016 | 0.000024 | 0.001088 | 0.000735 | 0.001075 | 0.000756 | 0.001105 | -0.278686 | -0.269031 | 0.040423 | 0.309454 | -0.218785 | -0.447228 | -0.027576 | 0.419652 | 0.271343 | 0.35356 | 1,626 | 1,290 | 0.001381 | 0.000773 | 0.7949 | -0.361073 | 0.200604 | 27.5 | 1.015 | 0.999 | 0 | 101.88 | 0 | absent | absent | 0 | 0 | 0 | 0.34118 | 0.328966 | 0.335073 | missense_variant | missense_variant | ENSG00000012048 | 0 | ENSG00000012048 | 0 | 0 | ENSG00000012048 | missense_variant | ENSG00000108830 | 20,477 | ENSG00000012048 | 2,763 | 2,763 | ENSG00000012048 | missense_variant | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | Cell fitness | Chemical-based transfection | Nuclease | SpCas9 | Single-dimensional data | Loss of function | Immortalized human cells | Direct sequencing | Single-segment (short read) | Endogenous locus library method | Molecular function | normal | normal | ExCALIBR calibration | STRONG | 1 | 0.312452 |
17 | 43,045,709 | A | G | true | missense_variant | BRCA1 | sge | urn:mavedb:00000097-0-2 | -1.343872 | BRCA1 | 17 | 41,197,726 | A | G | NM_007294.3 | 5561 | T | C | c.5561T>C | 1,854 | L | P | p.L1854P | Missense | -1.343872 | LOF | 0.992373 | X23 | 3 | 371 | 2,599 | 868 | 2,300 | 584 | 0.000018 | 0.000994 | 0.000745 | 0.000318 | 0.000526 | 0.000214 | -0.13019 | -0.269031 | -1.586619 | -1.317588 | -0.611741 | -0.447228 | -2.266111 | -1.818883 | -1.155321 | -1.532422 | 747 | 424 | 0.000634 | 0.000254 | -0.345683 | -1.443291 | -0.919132 | 28.3 | 1.015 | 1 | 0 | 22.34 | 15 | Uncertain significance | Uncertain significance | 0 | 0 | 0 | -1.61277 | -1.607862 | -1.610316 | missense_variant | missense_variant | ENSG00000012048 | 0 | ENSG00000012048 | 0 | 0 | ENSG00000012048 | missense_variant | ENSG00000108830 | 20,477 | ENSG00000012048 | 2,763 | 2,763 | ENSG00000012048 | missense_variant | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | Cell fitness | Chemical-based transfection | Nuclease | SpCas9 | Single-dimensional data | Loss of function | Immortalized human cells | Direct sequencing | Single-segment (short read) | Endogenous locus library method | Molecular function | abnormal | abnormal | ExCALIBR calibration | STRONG | 1 | -1.343872 |
17 | 43,045,709 | A | T | false | missense_variant | BRCA1 | sge | urn:mavedb:00000097-0-2 | 0.259387 | BRCA1 | 17 | 41,197,726 | A | T | NM_007294.3 | 5561 | T | A | c.5561T>A | 1,854 | L | Q | p.L1854Q | Missense | 0.259387 | FUNC | 0 | X23 | 2 | 469 | 2,935 | 2,514 | 2,847 | 4,357 | 0.000012 | 0.001257 | 0.000841 | 0.000921 | 0.000651 | 0.001596 | -0.292954 | -0.269031 | -0.39057 | -0.121539 | -0.642101 | -0.447228 | 0.295015 | 0.742243 | -0.106571 | 0.625345 | 738 | 299 | 0.000627 | 0.000179 | -0.538574 | -2.255018 | -1.306671 | 27 | 1.015 | 0.999 | 0 | 70.81 | 0 | absent | absent | 0 | 0 | 0 | 0.958219 | 0.264684 | 0.611451 | missense_variant | missense_variant | ENSG00000012048 | 0 | ENSG00000012048 | 0 | 0 | ENSG00000012048 | missense_variant | ENSG00000108830 | 20,477 | ENSG00000012048 | 2,763 | 2,763 | ENSG00000012048 | missense_variant | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | Cell fitness | Chemical-based transfection | Nuclease | SpCas9 | Single-dimensional data | Loss of function | Immortalized human cells | Direct sequencing | Single-segment (short read) | Endogenous locus library method | Molecular function | normal | normal | ExCALIBR calibration | STRONG | 1 | 0.259387 |
17 | 43,045,710 | G | C | false | missense_variant | BRCA1 | sge | urn:mavedb:00000097-0-2 | 0.158476 | BRCA1 | 17 | 41,197,727 | G | C | NM_007294.3 | 5560 | C | G | c.5560C>G | 1,854 | L | V | p.L1854V | Missense | 0.158476 | FUNC | 0 | X23 | 37 | 325 | 2,449 | 2,577 | 2,384 | 1,706 | 0.000218 | 0.000871 | 0.000702 | 0.000944 | 0.000545 | 0.000625 | -0.024974 | -0.263925 | 0.174286 | 0.438211 | -0.369011 | -0.448685 | -0.528554 | -0.07987 | 0.384244 | -0.067291 | 805 | 1,366 | 0.000684 | 0.000819 | -0.152038 | 0.19278 | -0.028092 | 26.6 | 2.766 | 0.991 | 0 | 74.52 | 0 | absent | absent | 0 | 0 | 0 | 0.843913 | -0.178899 | 0.332507 | missense_variant | missense_variant | ENSG00000012048 | 0 | ENSG00000012048 | 0 | 0 | ENSG00000012048 | missense_variant | ENSG00000108830 | 20,478 | ENSG00000012048 | 2,762 | 2,762 | ENSG00000012048 | missense_variant | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | Cell fitness | Chemical-based transfection | Nuclease | SpCas9 | Single-dimensional data | Loss of function | Immortalized human cells | Direct sequencing | Single-segment (short read) | Endogenous locus library method | Molecular function | normal | normal | ExCALIBR calibration | STRONG | 1 | 0.158476 |
17 | 43,045,710 | G | T | false | missense_variant | BRCA1 | sge | urn:mavedb:00000097-0-2 | -0.040534 | BRCA1 | 17 | 41,197,727 | G | T | NM_007294.3 | 5560 | C | A | c.5560C>A | 1,854 | L | M | p.L1854M | Missense | -0.040534 | FUNC | 0.000001 | X23 | 1 | 299 | 2,042 | 1,688 | 1,819 | 1,611 | 0.000006 | 0.000801 | 0.000585 | 0.000618 | 0.000416 | 0.00059 | -0.16689 | -0.263925 | -0.315797 | -0.051872 | -0.638956 | -0.448685 | -0.490921 | -0.042236 | -0.045484 | -0.035585 | 572 | 992 | 0.000486 | 0.000595 | -0.382802 | 0.121473 | -0.160065 | 27.2 | 2.766 | 0.999 | 0 | 95.8 | 0 | absent | absent | 0 | 0 | 0 | -0.30013 | -0.380881 | -0.340505 | missense_variant | missense_variant | ENSG00000012048 | 0 | ENSG00000012048 | 0 | 0 | ENSG00000012048 | missense_variant | ENSG00000108830 | 20,478 | ENSG00000012048 | 2,762 | 2,762 | ENSG00000012048 | missense_variant | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | Cell fitness | Chemical-based transfection | Nuclease | SpCas9 | Single-dimensional data | Loss of function | Immortalized human cells | Direct sequencing | Single-segment (short read) | Endogenous locus library method | Molecular function | normal | normal | ExCALIBR calibration | STRONG | 1 | -0.040534 |
17 | 43,045,712 | T | A | false | missense_variant | BRCA1 | sge | urn:mavedb:00000097-0-2 | -0.627988 | BRCA1 | 17 | 41,197,729 | T | A | NM_007294.3 | 5558 | A | T | c.5558A>T | 1,853 | Y | F | p.Y1853F | Missense | -0.627988 | FUNC | 0.001739 | X23 | 4 | 574 | 3,376 | 2,274 | 4,172 | 1,825 | 0.000024 | 0.001539 | 0.000967 | 0.000833 | 0.000955 | 0.000669 | -0.382463 | -0.222968 | -0.826785 | -0.603817 | -0.382267 | -0.389554 | -1.251887 | -0.862333 | -0.529455 | -0.726522 | 1,149 | 2,418 | 0.000976 | 0.00145 | -0.101842 | 0.209282 | 0.001764 | 28.7 | 2.232 | 0.997 | 0 | -21.61 | 15 | absent | absent | 0 | 0 | 0 | -0.554934 | -0.985728 | -0.770331 | missense_variant | missense_variant | ENSG00000012048 | 0 | ENSG00000012048 | 0 | 0 | ENSG00000012048 | missense_variant | ENSG00000108830 | 20,480 | ENSG00000012048 | 2,760 | 2,760 | ENSG00000012048 | missense_variant | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | Cell fitness | Chemical-based transfection | Nuclease | SpCas9 | Single-dimensional data | Loss of function | Immortalized human cells | Direct sequencing | Single-segment (short read) | Endogenous locus library method | Molecular function | normal | normal | ExCALIBR calibration | STRONG | 1 | -0.627988 |
17 | 43,045,712 | T | C | true | missense_variant | BRCA1 | sge | urn:mavedb:00000097-0-2 | -2.763438 | BRCA1 | 17 | 41,197,729 | T | C | NM_007294.3 | 5558 | A | G | c.5558A>G | 1,853 | Y | C | p.Y1853C | Missense | -2.763438 | LOF | 1 | X23 | 1 | 454 | 2,965 | 494 | 1,713 | 165 | 0.000006 | 0.001217 | 0.00085 | 0.000181 | 0.000392 | 0.00006 | -0.231387 | -0.222968 | -2.691076 | -2.468108 | -1.328123 | -0.389554 | -4.380887 | -3.991333 | -2.164151 | -3.362726 | 326 | 746 | 0.000277 | 0.000447 | -1.731994 | -0.203071 | -0.783032 | 27 | 2.232 | 1 | 0 | -193.72 | 65 | Conflicting interpretations of pathogenicity | Conflicting interpretations of pathogenicity | 0 | 0 | 0 | null | null | null | missense_variant | missense_variant | ENSG00000012048 | 0 | ENSG00000012048 | 0 | 0 | ENSG00000012048 | missense_variant | ENSG00000108830 | 20,480 | ENSG00000012048 | 2,760 | 2,760 | ENSG00000012048 | missense_variant | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | Cell fitness | Chemical-based transfection | Nuclease | SpCas9 | Single-dimensional data | Loss of function | Immortalized human cells | Direct sequencing | Single-segment (short read) | Endogenous locus library method | Molecular function | abnormal | abnormal | ExCALIBR calibration | STRONG | 1 | -2.763438 |
17 | 43,045,712 | T | G | true | missense_variant | BRCA1 | sge | urn:mavedb:00000097-0-2 | -1.698237 | BRCA1 | 17 | 41,197,729 | T | G | NM_007294.3 | 5558 | A | C | c.5558A>C | 1,853 | Y | S | p.Y1853S | Missense | -1.698237 | LOF | 0.999985 | X23 | 2 | 505 | 4,562 | 922 | 2,327 | 618 | 0.000012 | 0.001354 | 0.001307 | 0.000338 | 0.000532 | 0.000226 | 0.236656 | -0.222968 | -1.944411 | -1.721443 | -1.039768 | -0.389554 | -2.629337 | -2.239783 | -1.509441 | -1.887033 | 762 | 289 | 0.000647 | 0.000173 | -1.12871 | -2.013123 | -1.62133 | 29.8 | 2.232 | 1 | 0 | -143.11 | 65 | absent | absent | 0 | 0 | 0 | null | null | null | missense_variant | missense_variant | ENSG00000012048 | 0 | ENSG00000012048 | 0 | 0 | ENSG00000012048 | missense_variant | ENSG00000108830 | 20,480 | ENSG00000012048 | 2,760 | 2,760 | ENSG00000012048 | missense_variant | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | Cell fitness | Chemical-based transfection | Nuclease | SpCas9 | Single-dimensional data | Loss of function | Immortalized human cells | Direct sequencing | Single-segment (short read) | Endogenous locus library method | Molecular function | abnormal | abnormal | ExCALIBR calibration | STRONG | 1 | -1.698237 |
17 | 43,045,713 | A | C | true | missense_variant | BRCA1 | sge | urn:mavedb:00000097-0-2 | -3.351372 | BRCA1 | 17 | 41,197,730 | A | C | NM_007294.3 | 5557 | T | G | c.5557T>G | 1,853 | Y | D | p.Y1853D | Missense | -3.351372 | LOF | 1 | X23 | 2 | 458 | 2,219 | 542 | 1,633 | 61 | 0.000012 | 0.001228 | 0.000636 | 0.000199 | 0.000374 | 0.000022 | -0.662165 | -0.200186 | -2.569949 | -2.369763 | -1.409779 | -0.339764 | -5.829127 | -5.489363 | -2.077917 | -4.624826 | 504 | 1,372 | 0.000428 | 0.000823 | -0.68532 | 0.744962 | 0.187504 | 28.4 | 2.232 | 1 | 0 | -159.94 | 65 | absent | absent | 0 | 0 | 0 | null | null | null | missense_variant | missense_variant | ENSG00000012048 | 0 | ENSG00000012048 | 0 | 0 | ENSG00000012048 | missense_variant | ENSG00000108830 | 20,481 | ENSG00000012048 | 2,759 | 2,759 | ENSG00000012048 | missense_variant | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | Cell fitness | Chemical-based transfection | Nuclease | SpCas9 | Single-dimensional data | Loss of function | Immortalized human cells | Direct sequencing | Single-segment (short read) | Endogenous locus library method | Molecular function | abnormal | abnormal | ExCALIBR calibration | STRONG | 1 | -3.351372 |
17 | 43,045,713 | A | G | true | missense_variant | BRCA1 | sge | urn:mavedb:00000097-0-2 | -1.652883 | BRCA1 | 17 | 41,197,730 | A | G | NM_007294.3 | 5557 | T | C | c.5557T>C | 1,853 | Y | H | p.Y1853H | Missense | -1.652883 | LOF | 0.999966 | X23 | 3 | 470 | 2,768 | 574 | 3,060 | 991 | 0.000018 | 0.00126 | 0.000793 | 0.00021 | 0.0007 | 0.000363 | -0.380544 | -0.200186 | -2.524505 | -2.324318 | -0.541085 | -0.339764 | -1.844436 | -1.504672 | -2.038069 | -1.267696 | 967 | 2,263 | 0.000821 | 0.001357 | -0.064162 | 0.560912 | 0.236147 | 28.6 | 2.232 | 1 | 0 | -83.33 | 65 | absent | absent | 0 | 0 | 0 | -0.636771 | -2.183043 | -1.409907 | missense_variant | missense_variant | ENSG00000012048 | 0 | ENSG00000012048 | 0 | 0 | ENSG00000012048 | missense_variant | ENSG00000108830 | 20,481 | ENSG00000012048 | 2,759 | 2,759 | ENSG00000012048 | missense_variant | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | Cell fitness | Chemical-based transfection | Nuclease | SpCas9 | Single-dimensional data | Loss of function | Immortalized human cells | Direct sequencing | Single-segment (short read) | Endogenous locus library method | Molecular function | abnormal | abnormal | ExCALIBR calibration | STRONG | 1 | -1.652883 |
17 | 43,045,713 | A | T | true | missense_variant | BRCA1 | sge | urn:mavedb:00000097-0-2 | -2.167195 | BRCA1 | 17 | 41,197,730 | A | T | NM_007294.3 | 5557 | T | A | c.5557T>A | 1,853 | Y | N | p.Y1853N | Missense | -2.167195 | LOF | 1 | X23 | 2 | 313 | 1,224 | 184 | 1,441 | 606 | 0.000012 | 0.000839 | 0.000351 | 0.000067 | 0.00033 | 0.000222 | -0.971286 | -0.200186 | -3.579351 | -3.379165 | -1.041048 | -0.339764 | -1.967505 | -1.627741 | -2.963008 | -1.371383 | 255 | 264 | 0.000217 | 0.000158 | -0.809941 | -1.452254 | -1.201627 | 28.8 | 2.232 | 1 | 0 | -142.23 | 65 | Uncertain significance | Uncertain significance | 0 | 0 | 0 | -4.262648 | -2.502011 | -3.382329 | missense_variant | missense_variant | ENSG00000012048 | 0 | ENSG00000012048 | 0 | 0 | ENSG00000012048 | missense_variant | ENSG00000108830 | 20,481 | ENSG00000012048 | 2,759 | 2,759 | ENSG00000012048 | missense_variant | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | Cell fitness | Chemical-based transfection | Nuclease | SpCas9 | Single-dimensional data | Loss of function | Immortalized human cells | Direct sequencing | Single-segment (short read) | Endogenous locus library method | Molecular function | abnormal | abnormal | ExCALIBR calibration | STRONG | 1 | -2.167195 |
17 | 43,045,715 | G | A | false | missense_variant | BRCA1 | sge | urn:mavedb:00000097-0-2 | -0.152108 | BRCA1 | 17 | 41,197,732 | G | A | NM_007294.3 | 5555 | C | T | c.5555C>T | 1,852 | T | I | p.T1852I | Missense | -0.152108 | FUNC | 0.000003 | X23 | 3 | 521 | 3,704 | 3,152 | 4,371 | 2,711 | 0.000018 | 0.001397 | 0.001061 | 0.001155 | 0.001 | 0.000993 | -0.108926 | -0.178677 | -0.215982 | -0.037306 | -0.175276 | -0.218934 | -0.541191 | -0.322257 | -0.032711 | -0.271504 | 1,097 | 4,266 | 0.000932 | 0.002558 | -0.302427 | 0.961127 | 0.444477 | 28.1 | 1.411 | 0.916 | 0 | 58.19 | 0 | Uncertain significance | Uncertain significance | 0 | 0 | 0 | 0.007085 | -0.817001 | -0.404958 | missense_variant | missense_variant | ENSG00000012048 | 0 | ENSG00000012048 | 0 | 0 | ENSG00000012048 | missense_variant | ENSG00000108830 | 20,483 | ENSG00000012048 | 2,757 | 2,757 | ENSG00000012048 | missense_variant | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | Cell fitness | Chemical-based transfection | Nuclease | SpCas9 | Single-dimensional data | Loss of function | Immortalized human cells | Direct sequencing | Single-segment (short read) | Endogenous locus library method | Molecular function | normal | normal | ExCALIBR calibration | STRONG | 1 | -0.152108 |
17 | 43,045,715 | G | C | false | missense_variant | BRCA1 | sge | urn:mavedb:00000097-0-2 | -0.131134 | BRCA1 | 17 | 41,197,732 | G | C | NM_007294.3 | 5555 | C | G | c.5555C>G | 1,852 | T | S | p.T1852S | Missense | -0.131134 | FUNC | 0.000002 | X23 | 3 | 547 | 3,416 | 3,328 | 4,185 | 2,929 | 0.000018 | 0.001466 | 0.000979 | 0.001219 | 0.000958 | 0.001073 | -0.29596 | -0.178677 | -0.207852 | -0.029175 | -0.308269 | -0.218934 | -0.499865 | -0.280931 | -0.025582 | -0.236687 | 904 | 2,646 | 0.000768 | 0.001586 | -0.464819 | 0.334792 | -0.04839 | 23.7 | 1.411 | 0.349 | 0.02 | 124.5 | 0 | absent | absent | 0 | 0 | 0 | 0.076613 | -0.176072 | -0.049729 | missense_variant | missense_variant | ENSG00000012048 | 0 | ENSG00000012048 | 0 | 0 | ENSG00000012048 | missense_variant | ENSG00000108830 | 20,483 | ENSG00000012048 | 2,757 | 2,757 | ENSG00000012048 | missense_variant | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | Cell fitness | Chemical-based transfection | Nuclease | SpCas9 | Single-dimensional data | Loss of function | Immortalized human cells | Direct sequencing | Single-segment (short read) | Endogenous locus library method | Molecular function | normal | normal | ExCALIBR calibration | STRONG | 1 | -0.131134 |
17 | 43,045,715 | G | T | false | missense_variant | BRCA1 | sge | urn:mavedb:00000097-0-2 | -0.0745 | BRCA1 | 17 | 41,197,732 | G | T | NM_007294.3 | 5555 | C | A | c.5555C>A | 1,852 | T | N | p.T1852N | Missense | -0.0745 | FUNC | 0.000001 | X23 | 5 | 408 | 2,319 | 2,150 | 3,037 | 2,785 | 0.000029 | 0.001094 | 0.000665 | 0.000788 | 0.000695 | 0.00102 | -0.431793 | -0.178677 | -0.415199 | -0.236522 | -0.347878 | -0.218934 | -0.149624 | 0.069309 | -0.207394 | 0.058394 | 1,019 | 521 | 0.000866 | 0.000312 | 0.266745 | -1.547085 | -0.526974 | 26.6 | 1.411 | 0.874 | 0 | 127.25 | 0 | absent | absent | 0 | 0 | 0 | 0.491096 | 0.711335 | 0.601215 | missense_variant | missense_variant | ENSG00000012048 | 0 | ENSG00000012048 | 0 | 0 | ENSG00000012048 | missense_variant | ENSG00000108830 | 20,483 | ENSG00000012048 | 2,757 | 2,757 | ENSG00000012048 | missense_variant | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | Cell fitness | Chemical-based transfection | Nuclease | SpCas9 | Single-dimensional data | Loss of function | Immortalized human cells | Direct sequencing | Single-segment (short read) | Endogenous locus library method | Molecular function | normal | normal | ExCALIBR calibration | STRONG | 1 | -0.0745 |
17 | 43,045,716 | T | A | false | missense_variant | BRCA1 | sge | urn:mavedb:00000097-0-2 | -0.235598 | BRCA1 | 17 | 41,197,733 | T | A | NM_007294.3 | 5554 | A | T | c.5554A>T | 1,852 | T | S | p.T1852S | Missense | -0.235598 | FUNC | 0.000008 | X23 | 4 | 503 | 3,895 | 3,128 | 4,001 | 2,296 | 0.000024 | 0.001348 | 0.001116 | 0.001146 | 0.000915 | 0.000841 | 0.014338 | -0.17897 | -0.176284 | 0.002686 | -0.252154 | -0.168094 | -0.730168 | -0.562074 | 0.002355 | -0.473551 | 1,007 | 608 | 0.000855 | 0.000365 | -0.498466 | -1.722011 | -1.116226 | 23.3 | 0.144 | 0.349 | 0.02 | 124.5 | 0 | absent | absent | 0 | 0 | 0 | 0.007455 | -0.51376 | -0.253152 | missense_variant | missense_variant | ENSG00000012048 | 0 | ENSG00000012048 | 0 | 0 | ENSG00000012048 | missense_variant | ENSG00000108830 | 20,484 | ENSG00000012048 | 2,756 | 2,756 | ENSG00000012048 | missense_variant | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | Cell fitness | Chemical-based transfection | Nuclease | SpCas9 | Single-dimensional data | Loss of function | Immortalized human cells | Direct sequencing | Single-segment (short read) | Endogenous locus library method | Molecular function | normal | normal | ExCALIBR calibration | STRONG | 1 | -0.235598 |
17 | 43,045,716 | T | C | false | missense_variant | BRCA1 | sge | urn:mavedb:00000097-0-2 | 0.309628 | BRCA1 | 17 | 41,197,733 | T | C | NM_007294.3 | 5554 | A | G | c.5554A>G | 1,852 | T | A | p.T1852A | Missense | 0.309628 | FUNC | 0 | X23 | 4 | 466 | 3,537 | 3,314 | 5,269 | 4,537 | 0.000024 | 0.001249 | 0.001014 | 0.001214 | 0.001206 | 0.001662 | -0.014531 | -0.17897 | 0.017277 | 0.196247 | 0.255243 | -0.168094 | 0.362676 | 0.53077 | 0.172079 | 0.447178 | 1,653 | 2,060 | 0.001404 | 0.001235 | 0.355654 | -0.358678 | -0.067091 | 9.563 | 0.144 | 0.205 | 0.84 | 127.25 | 0 | Uncertain significance | Uncertain significance | 0 | 0 | 0 | -0.565691 | 0.019024 | -0.273333 | missense_variant | missense_variant | ENSG00000012048 | 0 | ENSG00000012048 | 0 | 0 | ENSG00000012048 | missense_variant | ENSG00000108830 | 20,484 | ENSG00000012048 | 2,756 | 2,756 | ENSG00000012048 | missense_variant | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | Cell fitness | Chemical-based transfection | Nuclease | SpCas9 | Single-dimensional data | Loss of function | Immortalized human cells | Direct sequencing | Single-segment (short read) | Endogenous locus library method | Molecular function | normal | normal | ExCALIBR calibration | STRONG | 1 | 0.309628 |
17 | 43,045,716 | T | G | false | missense_variant | BRCA1 | sge | urn:mavedb:00000097-0-2 | -0.067412 | BRCA1 | 17 | 41,197,733 | T | G | NM_007294.3 | 5554 | A | C | c.5554A>C | 1,852 | T | P | p.T1852P | Missense | -0.067412 | FUNC | 0.000001 | X23 | 1 | 293 | 2,143 | 1,905 | 2,162 | 1,684 | 0.000006 | 0.000785 | 0.000614 | 0.000698 | 0.000495 | 0.000617 | -0.067996 | -0.17897 | -0.112076 | 0.066894 | -0.36049 | -0.168094 | -0.397741 | -0.229647 | 0.058656 | -0.193479 | 510 | 381 | 0.000433 | 0.000228 | -0.617969 | -1.508297 | -1.112932 | 19.1 | 0.144 | 0.022 | 0.08 | 125.63 | 0 | absent | absent | 0 | 0 | 0 | 1.134452 | -0.383096 | 0.375678 | missense_variant | missense_variant | ENSG00000012048 | 0 | ENSG00000012048 | 0 | 0 | ENSG00000012048 | missense_variant | ENSG00000108830 | 20,484 | ENSG00000012048 | 2,756 | 2,756 | ENSG00000012048 | missense_variant | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | Cell fitness | Chemical-based transfection | Nuclease | SpCas9 | Single-dimensional data | Loss of function | Immortalized human cells | Direct sequencing | Single-segment (short read) | Endogenous locus library method | Molecular function | normal | normal | ExCALIBR calibration | STRONG | 1 | -0.067412 |
17 | 43,045,717 | G | C | false | missense_variant | BRCA1 | sge | urn:mavedb:00000097-0-2 | 0.007962 | BRCA1 | 17 | 41,197,734 | G | C | NM_007294.3 | 5553 | C | G | c.5553C>G | 1,851 | D | E | p.D1851E | Missense | 0.007962 | FUNC | 0 | X23 | 1 | 292 | 2,343 | 2,110 | 2,716 | 1,770 | 0.000006 | 0.000783 | 0.000671 | 0.000773 | 0.000621 | 0.000648 | 0.065662 | -0.167522 | 0.040308 | 0.207831 | -0.026441 | -0.12355 | -0.320951 | -0.197401 | 0.182235 | -0.166312 | 378 | 1,017 | 0.000321 | 0.00061 | -1.178805 | -0.420957 | -0.790587 | 23.4 | 0.349 | 0.022 | 0 | 120.86 | 0 | absent | absent | 0 | 0 | 0 | -0.092468 | 0.175511 | 0.041522 | missense_variant | missense_variant | ENSG00000012048 | 0 | ENSG00000012048 | 0 | 0 | ENSG00000012048 | missense_variant | ENSG00000108830 | 20,485 | ENSG00000012048 | 2,755 | 2,755 | ENSG00000012048 | missense_variant | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | Cell fitness | Chemical-based transfection | Nuclease | SpCas9 | Single-dimensional data | Loss of function | Immortalized human cells | Direct sequencing | Single-segment (short read) | Endogenous locus library method | Molecular function | normal | normal | ExCALIBR calibration | STRONG | 1 | 0.007962 |
17 | 43,045,717 | G | T | false | missense_variant | BRCA1 | sge | urn:mavedb:00000097-0-2 | -0.236928 | BRCA1 | 17 | 41,197,734 | G | T | NM_007294.3 | 5553 | C | A | c.5553C>A | 1,851 | D | E | p.D1851E | Missense | -0.236928 | FUNC | 0.000008 | X23 | 2 | 538 | 3,290 | 2,184 | 4,175 | 3,972 | 0.000012 | 0.001442 | 0.000943 | 0.0008 | 0.000955 | 0.001455 | -0.326246 | -0.167522 | -0.7916 | -0.624077 | -0.287786 | -0.12355 | -0.036473 | 0.087077 | -0.54722 | 0.073363 | 1,580 | 1,100 | 0.001342 | 0.00066 | 0.394931 | -0.928066 | -0.256071 | 23.6 | 0.349 | 0.022 | 0 | 120.86 | 0 | absent | absent | 0 | 0 | 0 | -0.565955 | 0.339982 | -0.112987 | missense_variant | missense_variant | ENSG00000012048 | 0 | ENSG00000012048 | 0 | 0 | ENSG00000012048 | missense_variant | ENSG00000108830 | 20,485 | ENSG00000012048 | 2,755 | 2,755 | ENSG00000012048 | missense_variant | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | Cell fitness | Chemical-based transfection | Nuclease | SpCas9 | Single-dimensional data | Loss of function | Immortalized human cells | Direct sequencing | Single-segment (short read) | Endogenous locus library method | Molecular function | normal | normal | ExCALIBR calibration | STRONG | 1 | -0.236928 |
17 | 43,045,718 | T | A | false | missense_variant | BRCA1 | sge | urn:mavedb:00000097-0-2 | -0.675032 | BRCA1 | 17 | 41,197,735 | T | A | NM_007294.3 | 5552 | A | T | c.5552A>T | 1,851 | D | V | p.D1851V | Missense | -0.675032 | FUNC | 0.003426 | X23 | 3 | 553 | 3,412 | 2,662 | 4,226 | 1,701 | 0.000018 | 0.001482 | 0.000978 | 0.000975 | 0.000967 | 0.000623 | -0.313389 | -0.156148 | -0.545735 | -0.389588 | -0.309943 | -0.10266 | -1.299629 | -1.196969 | -0.341608 | -1.008455 | 712 | 719 | 0.000605 | 0.000431 | -0.807575 | -1.559022 | -1.245983 | 26.8 | 0.103 | 0.918 | 0 | 71.64 | 0 | absent | absent | 0 | 0 | 0 | -1.223956 | -0.635848 | -0.929902 | missense_variant | missense_variant | ENSG00000012048 | 0 | ENSG00000012048 | 0 | 0 | ENSG00000012048 | missense_variant | ENSG00000108830 | 20,486 | ENSG00000012048 | 2,754 | 2,754 | ENSG00000012048 | missense_variant | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | Cell fitness | Chemical-based transfection | Nuclease | SpCas9 | Single-dimensional data | Loss of function | Immortalized human cells | Direct sequencing | Single-segment (short read) | Endogenous locus library method | Molecular function | normal | normal | ExCALIBR calibration | MODERATE_PLUS | 1 | -0.675032 |
17 | 43,045,718 | T | C | false | missense_variant | BRCA1 | sge | urn:mavedb:00000097-0-2 | -0.328078 | BRCA1 | 17 | 41,197,735 | T | C | NM_007294.3 | 5552 | A | G | c.5552A>G | 1,851 | D | G | p.D1851G | Missense | -0.328078 | FUNC | 0.000028 | X23 | 1 | 436 | 3,906 | 1,861 | 4,024 | 2,690 | 0.000006 | 0.001169 | 0.001119 | 0.000682 | 0.000921 | 0.000985 | 0.224637 | -0.156148 | -0.719217 | -0.563069 | -0.037654 | -0.10266 | -0.295454 | -0.192795 | -0.493725 | -0.162431 | 2,113 | 2,032 | 0.001795 | 0.001218 | 0.566695 | 0.010477 | 0.213299 | 26 | 0.103 | 0.915 | 0.01 | 69.19 | 0 | absent | absent | 0 | 0 | 0 | 0.947611 | 0.311702 | 0.629657 | missense_variant | missense_variant | ENSG00000012048 | 0 | ENSG00000012048 | 0 | 0 | ENSG00000012048 | missense_variant | ENSG00000108830 | 20,486 | ENSG00000012048 | 2,754 | 2,754 | ENSG00000012048 | missense_variant | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | Cell fitness | Chemical-based transfection | Nuclease | SpCas9 | Single-dimensional data | Loss of function | Immortalized human cells | Direct sequencing | Single-segment (short read) | Endogenous locus library method | Molecular function | normal | normal | ExCALIBR calibration | STRONG | 1 | -0.328078 |
17 | 43,045,718 | T | G | false | missense_variant | BRCA1 | sge | urn:mavedb:00000097-0-2 | -0.243174 | BRCA1 | 17 | 41,197,735 | T | G | NM_007294.3 | 5552 | A | C | c.5552A>C | 1,851 | D | A | p.D1851A | Missense | -0.243174 | FUNC | 0.000009 | X23 | 2 | 620 | 4,091 | 2,754 | 5,584 | 4,220 | 0.000012 | 0.001662 | 0.001172 | 0.001009 | 0.001278 | 0.001546 | -0.216542 | -0.156148 | -0.661706 | -0.505558 | -0.072925 | -0.10266 | -0.153758 | -0.051098 | -0.443297 | -0.04305 | 1,021 | 885 | 0.000867 | 0.000531 | -0.549377 | -1.661343 | -1.128005 | 24 | 0.103 | 0.778 | 0.09 | 87.36 | 0 | absent | absent | 0 | 0 | 0 | -0.534551 | -0.151315 | -0.342933 | missense_variant | missense_variant | ENSG00000012048 | 0 | ENSG00000012048 | 0 | 0 | ENSG00000012048 | missense_variant | ENSG00000108830 | 20,486 | ENSG00000012048 | 2,754 | 2,754 | ENSG00000012048 | missense_variant | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | Cell fitness | Chemical-based transfection | Nuclease | SpCas9 | Single-dimensional data | Loss of function | Immortalized human cells | Direct sequencing | Single-segment (short read) | Endogenous locus library method | Molecular function | normal | normal | ExCALIBR calibration | STRONG | 1 | -0.243174 |
17 | 43,045,719 | C | A | false | missense_variant | BRCA1 | sge | urn:mavedb:00000097-0-2 | -0.636701 | BRCA1 | 17 | 41,197,736 | C | A | NM_007294.3 | 5551 | G | T | c.5551G>T | 1,851 | D | Y | p.D1851Y | Missense | -0.636701 | FUNC | 0.00197 | X23 | 2 | 471 | 2,536 | 1,997 | 3,020 | 1,780 | 0.000012 | 0.001263 | 0.000727 | 0.000732 | 0.000691 | 0.000652 | -0.509899 | -0.147192 | -0.728859 | -0.581667 | -0.563134 | -0.096513 | -1.002582 | -0.906069 | -0.510032 | -0.763369 | 1,232 | 2,239 | 0.001046 | 0.001342 | 0.411541 | 0.564513 | 0.422211 | 32 | 1.474 | 0.973 | 0 | 77.44 | 0 | absent | absent | 0 | 0 | 0 | -0.851787 | -0.651456 | -0.751621 | missense_variant | missense_variant | ENSG00000012048 | 0 | ENSG00000012048 | 0 | 0 | ENSG00000012048 | missense_variant | ENSG00000108830 | 20,487 | ENSG00000012048 | 2,753 | 2,753 | ENSG00000012048 | missense_variant | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | Cell fitness | Chemical-based transfection | Nuclease | SpCas9 | Single-dimensional data | Loss of function | Immortalized human cells | Direct sequencing | Single-segment (short read) | Endogenous locus library method | Molecular function | normal | normal | ExCALIBR calibration | STRONG | 1 | -0.636701 |
17 | 43,045,719 | C | G | false | missense_variant | BRCA1 | sge | urn:mavedb:00000097-0-2 | -0.044297 | BRCA1 | 17 | 41,197,736 | C | G | NM_007294.3 | 5551 | G | C | c.5551G>C | 1,851 | D | H | p.D1851H | Missense | -0.044297 | FUNC | 0.000001 | X23 | 3 | 551 | 3,726 | 2,609 | 6,267 | 4,920 | 0.000018 | 0.001477 | 0.001068 | 0.000956 | 0.001434 | 0.001802 | -0.181152 | -0.147192 | -0.569522 | -0.42233 | 0.263767 | -0.096513 | 0.237874 | 0.334387 | -0.370318 | 0.281723 | 821 | 2,894 | 0.000697 | 0.001735 | -0.72908 | -0.118503 | -0.438203 | 28.4 | 1.474 | 0.957 | 0 | 120.86 | 0 | absent | absent | 0 | 0 | 0 | 0.961531 | 0.144857 | 0.553194 | missense_variant | missense_variant | ENSG00000012048 | 0 | ENSG00000012048 | 0 | 0 | ENSG00000012048 | missense_variant | ENSG00000108830 | 20,487 | ENSG00000012048 | 2,753 | 2,753 | ENSG00000012048 | missense_variant | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | Cell fitness | Chemical-based transfection | Nuclease | SpCas9 | Single-dimensional data | Loss of function | Immortalized human cells | Direct sequencing | Single-segment (short read) | Endogenous locus library method | Molecular function | normal | normal | ExCALIBR calibration | STRONG | 1 | -0.044297 |
17 | 43,045,719 | C | T | false | missense_variant | BRCA1 | sge | urn:mavedb:00000097-0-2 | -0.253026 | BRCA1 | 17 | 41,197,736 | C | T | NM_007294.3 | 5551 | G | A | c.5551G>A | 1,851 | D | N | p.D1851N | Missense | -0.253026 | FUNC | 0.00001 | X23 | 6 | 443 | 4,951 | 2,204 | 3,196 | 2,665 | 0.000035 | 0.001187 | 0.001419 | 0.000808 | 0.000731 | 0.000976 | 0.543686 | -0.147192 | -0.498149 | -0.350957 | -0.392995 | -0.096513 | -0.331904 | -0.23539 | -0.307735 | -0.198318 | 868 | 1,314 | 0.000737 | 0.000788 | -1.058859 | -0.286095 | -0.660596 | 32 | 1.474 | 0.778 | 0.01 | 120.86 | 0 | absent | absent | 0 | 0 | 0 | -0.589234 | -0.32969 | -0.459462 | missense_variant | missense_variant | ENSG00000012048 | 0 | ENSG00000012048 | 0 | 0 | ENSG00000012048 | missense_variant | ENSG00000108830 | 20,487 | ENSG00000012048 | 2,753 | 2,753 | ENSG00000012048 | missense_variant | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | Cell fitness | Chemical-based transfection | Nuclease | SpCas9 | Single-dimensional data | Loss of function | Immortalized human cells | Direct sequencing | Single-segment (short read) | Endogenous locus library method | Molecular function | normal | normal | ExCALIBR calibration | STRONG | 1 | -0.253026 |
17 | 43,045,721 | A | C | false | missense_variant | BRCA1 | sge | urn:mavedb:00000097-0-2 | -0.185898 | BRCA1 | 17 | 41,197,738 | A | C | NM_007294.3 | 5549 | T | G | c.5549T>G | 1,850 | L | R | p.L1850R | Missense | -0.185898 | FUNC | 0.000004 | X23 | 2 | 356 | 2,650 | 1,556 | 3,565 | 2,647 | 0.000012 | 0.000954 | 0.000759 | 0.00057 | 0.000816 | 0.00097 | -0.042612 | -0.15148 | -0.685002 | -0.533521 | 0.080069 | -0.14022 | -0.026251 | 0.113969 | -0.467816 | 0.096019 | 1,082 | 655 | 0.000919 | 0.000393 | 0.160802 | -1.448129 | -0.577504 | 29.3 | 2.232 | 0.998 | 0 | -74.87 | 45 | absent | absent | 0 | 0 | 0 | 0.206275 | 0.114232 | 0.160254 | missense_variant | missense_variant | ENSG00000012048 | 0 | ENSG00000012048 | 0 | 0 | ENSG00000012048 | missense_variant | ENSG00000108830 | 20,489 | ENSG00000012048 | 2,751 | 2,751 | ENSG00000012048 | missense_variant | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | Cell fitness | Chemical-based transfection | Nuclease | SpCas9 | Single-dimensional data | Loss of function | Immortalized human cells | Direct sequencing | Single-segment (short read) | Endogenous locus library method | Molecular function | normal | normal | ExCALIBR calibration | STRONG | 1 | -0.185898 |
End of preview. Expand in Data Studio
evals_sge
Variant-effect-prediction benchmark of saturation genome editing (SGE) function
scores. SGE edits the endogenous genomic locus (CRISPR-HDR, typically in haploid
HAP1 cells), so every assayed SNV has a direct experimental functional measurement
in genomic coordinates — an axis orthogonal to the clinical/population/statistical
labels of the other evals_* datasets, and one that covers near-exon noncoding
(splice-region, proximal-intronic) SNVs, not just missense.
No matching, no subsampling. The trivially-deleterious HIGH-impact consequences
(canonical splice, nonsense, frameshift, …) are dropped (exclude_consequences), and v2
(#297) further keeps only the
missense + splicing consequence groups — the two where the SGE assay actually
measures function. v3 (#301)
adds a binary label (True = impactful = calibrated abnormal, False =
normal) and keeps only label-non-null variants — dropping intermediate and
uncalibrated rows (all of BRCA2) — so this is a clean classification benchmark scored by
AUPRC. Every original author column is preserved under an author_ prefix
(125 columns), so no source metadata is lost.
Studies
One row per (gene × study). mavedb_urn is stamped on every variant so (gene, mavedb_urn) identifies the exact source.
| Gene | MaveDB accession | Study | Build | Variants | Function score | Classification |
|---|---|---|---|---|---|---|
| BRCA1 | urn:mavedb:00000097-0-2 |
Findlay et al. 2018, Nature 562:217–222 | hg19 → GRCh38 (lifted) | 2,751 | author_function_score_mean |
author_func_class (FUNC / INT / LOF) |
| DDX3X | urn:mavedb:00000658-0-1 |
Saturation genome editing of DDX3X (2023) | GRCh38 (c.→g.) | 5,556 | author_score |
author_sge_prediction_of_variant_function_in_ndd_context |
| BAP1 | urn:mavedb:00000662-0-1 |
Waters et al. 2024 — BAP1 SGE | GRCh38 (c.→g.) | 5,722 | author_score |
— |
| RAD51C | urn:mavedb:00000673-0-1 |
Saturation genome editing of RAD51C (2024) | GRCh38 (c.→g.) | 2,899 | author_score |
author_functional_classification |
| VHL | urn:mavedb:00000675-a-1 |
VHL SGE — functional spectrum (2024) | GRCh38 (c.→g.) | 1,274 | author_score |
— |
| BARD1 | urn:mavedb:00001250-a-1 |
Saturation genome editing of BARD1 (medRxiv 2025) | GRCh38 | 6,065 | author_score |
author_functional_consequence |
| PALB2 | urn:mavedb:00001259-a-1 |
Saturation genome editing of PALB2 (MaveDB) | GRCh38 | 5,681 | author_score |
author_functional_consequence |
| RAD51D | urn:mavedb:00001260-a-1 |
Saturation genome editing of RAD51D (MaveDB) | GRCh38 | 2,403 | author_score |
author_functional_consequence |
| CTCF | urn:mavedb:00001262-a-1 |
Saturation genome editing of CTCF (MaveDB) | GRCh38 | 3,142 | author_score |
author_functional_consequence |
| XRCC2 | urn:mavedb:00001264-a-1 |
Saturation genome editing of XRCC2 (MaveDB) | GRCh38 | 1,858 | author_score |
author_functional_consequence |
| SFPQ | urn:mavedb:00001265-a-1 |
Saturation genome editing of SFPQ (MaveDB) | GRCh38 | 1,390 | author_score |
author_functional_consequence |
Assay characteristics
MaveDB annotates each experiment with controlled-vocabulary assay facts,
captured verbatim on every variant as constant-per-gene assay_* columns (the full
keyword set; the table surfaces the decision-relevant ones).
| Gene | Assay readout | Mechanism | Molecular mechanism | Model system | Library mechanism |
|---|---|---|---|---|---|
| BAP1 | Cell fitness | Loss of function | — | Immortalized human cells | Nuclease |
| BARD1 | Cell proliferation assay | Loss of function | — | Immortalized human cells | Nuclease |
| BRCA1 | Cell fitness | Loss of function | Molecular function | Immortalized human cells | Nuclease |
| CTCF | Cell proliferation assay | Loss of function | — | Immortalized human cells | Nuclease |
| DDX3X | Cell fitness | Loss of function | Molecular function | Immortalized human cells | Nuclease |
| PALB2 | Cell proliferation assay | Loss of function | — | Immortalized human cells | Nuclease |
| RAD51C | Cell fitness | Loss of function | — | Immortalized human cells | Nuclease |
| RAD51D | Cell morphology assay | Loss of function | — | Immortalized human cells | Nuclease |
| SFPQ | Cell proliferation assay | Loss of function | — | Immortalized human cells | Nuclease |
| VHL | Cell fitness | Loss of function | — | Immortalized human cells | Nuclease |
| XRCC2 | Cell proliferation assay | Loss of function | — | Immortalized human cells | Nuclease |
Every MaveDB-annotated study is a loss-of-function assay (the Mechanism
column): a depletion / fitness screen reading out a variant's effect on cell
survival or growth in immortalized human cells, with the variant library
written into the endogenous locus by a CRISPR nuclease (SpCas9).
Splice-disrupting and NMD-triggering variants are therefore captured by
construction — the endogenous readout reflects mis-splicing and
nonsense-mediated decay — so MaveDB exposes no separate "detects splicing / NMD"
flag. BRCA2 (urn:mavedb:00001225-a-1) is the one study MaveDB leaves
unannotated, so its assay_* cells are blank.
Score calibration
MaveDB attaches score calibrations — threshold schemes mapping the continuous
function score onto functional classes. Two flavors appear here: investigator-provided
functional classes (the authors' own normal / abnormal cutoffs) and ClinGen /
ExCALIBR ACMG calibrations (clinically-calibrated thresholds that assign each score
bin an ACMG functional-evidence strength — PS3 pathogenic / BS3 benign, graded
SUPPORTING → VERY_STRONG, under a prior_probability_pathogenicity OddsPath
prior). 33 schemes are captured across the 11 calibrated genes.
| Gene | Calibration schemes | ACMG evidence strengths |
|---|---|---|
| BAP1 | 6 | SUPPORTING, MODERATE, MODERATE_PLUS, STRONG |
| BARD1 | 2 | SUPPORTING, MODERATE, MODERATE_PLUS, STRONG, VERY_STRONG |
| BRCA1 | 6 | SUPPORTING, MODERATE, MODERATE_PLUS, STRONG |
| CTCF | 2 | SUPPORTING, MODERATE, MODERATE_PLUS, STRONG |
| DDX3X | 1 | STRONG |
| PALB2 | 2 | SUPPORTING, MODERATE, MODERATE_PLUS, STRONG |
| RAD51C | 4 | SUPPORTING, MODERATE, MODERATE_PLUS, STRONG, VERY_STRONG |
| RAD51D | 2 | SUPPORTING, MODERATE, MODERATE_PLUS, STRONG |
| SFPQ | 1 | — |
| VHL | 5 | SUPPORTING, MODERATE, MODERATE_PLUS, STRONG |
| XRCC2 | 2 | SUPPORTING, MODERATE, MODERATE_PLUS, STRONG, VERY_STRONG |
The full, tidy long-format calibration table — one row per (gene × calibration ×
functional class), with the score range, variant count, GO call
(normal / abnormal / not_specified), ACMG criterion / strength / signed points, the
OddsPath prior, and threshold-source PMIDs — ships as calibrations.parquet
alongside the splits. BRCA2 has no MaveDB calibrations.
calibrations.parquet columns
| Column | Type | Description |
|---|---|---|
gene, mavedb_urn |
str | Study identifier (joins to the splits). |
calibration_title |
str | Scheme name (e.g. Investigator-provided functional classes, ExCALIBR calibration). |
research_use_only |
bool | MaveDB research-use-only flag for the scheme. |
baseline_score |
float | Scheme baseline (often the synonymous/normal anchor); null when not score-range based. |
prior_probability_pathogenicity |
float | OddsPath prior for the ACMG schemes; null otherwise. |
threshold_source_pmids |
str | Comma-joined PubMed IDs the thresholds derive from. |
class_label |
str | Functional class name (e.g. Functional, PS3 Strong (5)). |
go_classification |
str | normal / abnormal / not_specified. |
range_lower, range_upper |
float | Score range for the class (null = open / not score-range based). |
inclusive_lower, inclusive_upper |
bool | Whether the range bounds are inclusive. |
variant_count |
int | Variants MaveDB places in the class. |
acmg_criterion |
str | PS3 (pathogenic) / BS3 (benign); null for non-ACMG schemes. |
acmg_evidence_strength |
str | SUPPORTING … VERY_STRONG. |
acmg_points |
int | ExCALIBR signed evidence points (negative = benign). |
Splits
Chromosome-parity split (same convention as the other evals_* datasets): odd
chromosomes + X → train, even + Y → test. SGE loci sit on whole chromosomes, so
this is a gene-level holdout (e.g. BRCA1·chr17 → train).
| Split | Variants | Abnormal | Normal | Chromosomes |
|---|---|---|---|---|
train |
23,853 | 3,526 | 20,327 | odd: 1, 3, …, X |
test |
14,888 | 1,459 | 13,429 | even: 2, 4, …, Y |
| total | 38,741 | 4,985 | 33,756 |
Columns
| Column | Type | Description |
|---|---|---|
chrom, pos, ref, alt |
str / int / str / str | Variant coordinates (1-based, GRCh38). |
gene |
str | Gene symbol. |
assay |
str | sge. |
mavedb_urn |
str | Canonical MaveDB accession for the source study (see the table above). |
label |
bool | The AUPRC target (v3, #301): True = impactful (calibrated abnormal), False = normal. The build keeps only label-non-null rows, so this is always a clean bool. |
function_score |
float | Each study's headline continuous functional score (raw, per-study scale — pool by rank, not raw value). |
function_direction, function_score_aligned |
int / float | Per-gene assay direction (+1 / −1, null if unresolved — BRCA2) and the direction-corrected score (function_direction × function_score) so "higher = more functional" holds across genes. Sourced from the assay (calibration ranges / author class), not the model. |
calibrated_class |
str | ClinGen/ExCALIBR-calibrated abnormal / intermediate / normal (or null), decided at build with an ExCALIBR-first policy (prefers the live calibration; never a dated ClinVar snapshot). |
calibration_scheme, acmg_strength |
str | The scheme behind calibrated_class (an ExCALIBR / investigator title, or author_class for the categorical-only gene) and the matched range's ACMG functional-evidence strength (SUPPORTING … VERY_STRONG). |
author_class_harmonized |
str | Each study's discrete functional class mapped to a common abnormal / intermediate / normal axis (null where a study ships none — BAP1, VHL, BRCA2). |
author_* |
mixed | Every original column from the source study, verbatim (slugified, author_-prefixed). The headline variables per study are listed in the table above — e.g. for BRCA1 author_function_score_mean (continuous) and author_func_class (FUNC/INT/LOF). Original coordinates are kept too (e.g. author_position_hg19). |
assay_* |
str | MaveDB 'assay facts' — the experiment's controlled-vocabulary keywords (assay readout, mechanism, model system, library mechanism, …), constant per gene. See Assay characteristics below; blank for the one unannotated study (BRCA2). |
subset, consequence_group |
str | Coarse consequence grouping the eval stratifies on (subset is an alias of consequence_group, matching the other evals_* datasets). The build keeps only the missense_variant + splicing groups. |
consequence, consequence_cre, consequence_final |
str | Ensembl VEP consequence (raw, with-CRE-class, and after TSS/exon-proximity recategorization); reference annotations. |
distance_tss_*, distance_exon_*, *_closest_gene_id |
int / str | Distances to nearest TSS / exon and the Ensembl gene IDs there; reference annotations. |
v3 (#301) derives the binary
label from calibrated_class (abnormal → True, normal → False) and filters to
label-non-null rows. The harmonized continuous columns v2 added —
function_direction / function_score_aligned, calibrated_class with its
calibration_scheme + acmg_strength, and author_class_harmonized — are kept for
provenance (the AUPRC eval reads only label). The authors' raw function_score and
every author_ column are preserved verbatim; per-study scales still differ, so any
continuous re-analysis should pool by rank, not raw value.
Provenance
Built by the marin-dna eval pipeline at commit
0ce78a4.
- Curation pipeline:
snakemake/evals - Rules:
snakemake/evals/workflow/rules/sge.smk - Loading + annotation:
src/marin_dna/pipelines/evals/sge.py
License
Released under the terms of its upstream sources; consult each source study (below) for redistribution and commercial-use terms.
Citation
If you use this benchmark, please cite the source SGE studies:
- BRCA1 — Findlay et al. 2018, Nature 562:217–222 (PMID 30209399); MaveDB
urn:mavedb:00000097-0-2 - DDX3X — Saturation genome editing of DDX3X (2023) (PMID 38057330); MaveDB
urn:mavedb:00000658-0-1 - BAP1 — Waters et al. 2024 — BAP1 SGE (PMID 38969833); MaveDB
urn:mavedb:00000662-0-1 - RAD51C — Saturation genome editing of RAD51C (2024) (PMID 39299233); MaveDB
urn:mavedb:00000673-0-1 - VHL — VHL SGE — functional spectrum (2024) (PMID 38969834); MaveDB
urn:mavedb:00000675-a-1 - BARD1 — Saturation genome editing of BARD1 (medRxiv 2025); MaveDB
urn:mavedb:00001250-a-1 - PALB2 — Saturation genome editing of PALB2 (MaveDB); MaveDB
urn:mavedb:00001259-a-1 - RAD51D — Saturation genome editing of RAD51D (MaveDB); MaveDB
urn:mavedb:00001260-a-1 - CTCF — Saturation genome editing of CTCF (MaveDB); MaveDB
urn:mavedb:00001262-a-1 - XRCC2 — Saturation genome editing of XRCC2 (MaveDB); MaveDB
urn:mavedb:00001264-a-1 - SFPQ — Saturation genome editing of SFPQ (MaveDB); MaveDB
urn:mavedb:00001265-a-1
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