Datasets:

wanglab
/

variant_effect_non_snv

question stringlengths 84 268	answer stringlengths 6 879	reference_sequence stringlengths 4.1k 4.1k	mutated_sequence stringlengths 4.1k 4.1k	cleaned_pathogenicity stringclasses 2 values	__index_level_0__ int64 67 343k
Mutation found at chromosome 1 position 1040717, gene AGRN (agrin): benign or pathogenic? If pathogenic, indicate the relevant disease(s).	pathogenic; ['Congenital_myasthenic_syndrome', 'Congenital_myasthenic_syndrome_8']	TGGTGCAGGGAGGTGACTGGGTCCTTGGCCATGGGGTTGGGACCTGGGGGGAACCATTGGTCCACAGGTCCAGCCGAAGCCCAGGAGAACAGCTGGCTGGGCATCAGCAGGTGCCCGTTGGATTTGGACTGGGAGTCCCAGGGCCTTGGACAAGGCAGGGCCAAAGGGAGAGGGAGATGCTGAGGGGAGAGAGAAGGGGAACCAGAAGGGAAGTGAAAGGGCCAGGGGTGCATGTGGTTTGAGTTTGATTTGAGCCAGGACGGGGGAAGGCCAGTGGTGATGACAGCCCTCATGACTATACTTACAGTGGCAGCAGACGG...	TGGTGCAGGGAGGTGACTGGGTCCTTGGCCATGGGGTTGGGACCTGGGGGGAACCATTGGTCCACAGGTCCAGCCGAAGCCCAGGAGAACAGCTGGCTGGGCATCAGCAGGTGCCCGTTGGATTTGGACTGGGAGTCCCAGGGCCTTGGACAAGGCAGGGCCAAAGGGAGAGGGAGATGCTGAGGGGAGAGAGAAGGGGAACCAGAAGGGAAGTGAAAGGGCCAGGGGTGCATGTGGTTTGAGTTTGATTTGAGCCAGGACGGGGGAAGGCCAGTGGTGATGACAGCCCTCATGACTATACTTACAGTGGCAGCAGACGG...	pathogenic	67
Evaluate if the mutation on chromosome 1 at position 1040819 in AGRN is benign or pathogenic. Disease name(s) if pathogenic?	pathogenic; ['Congenital_myasthenic_syndrome_8']	ATCAGCAGGTGCCCGTTGGATTTGGACTGGGAGTCCCAGGGCCTTGGACAAGGCAGGGCCAAAGGGAGAGGGAGATGCTGAGGGGAGAGAGAAGGGGAACCAGAAGGGAAGTGAAAGGGCCAGGGGTGCATGTGGTTTGAGTTTGATTTGAGCCAGGACGGGGGAAGGCCAGTGGTGATGACAGCCCTCATGACTATACTTACAGTGGCAGCAGACGGGCCACATAGCGCTGTGTGCTGGGCACCCTCTAAGCTTTGCAGATACTGGCCCATTTAACCCCACAATCCTGGGAGGTAGGTCCTATTGCTCCTATTCACCGA...	ATCAGCAGGTGCCCGTTGGATTTGGACTGGGAGTCCCAGGGCCTTGGACAAGGCAGGGCCAAAGGGAGAGGGAGATGCTGAGGGGAGAGAGAAGGGGAACCAGAAGGGAAGTGAAAGGGCCAGGGGTGCATGTGGTTTGAGTTTGATTTGAGCCAGGACGGGGGAAGGCCAGTGGTGATGACAGCCCTCATGACTATACTTACAGTGGCAGCAGACGGGCCACATAGCGCTGTGTGCTGGGCACCCTCTAAGCTTTGCAGATACTGGCCCATTTAACCCCACAATCCTGGGAGGTAGGTCCTATTGCTCCTATTCACCGA...	pathogenic	69
A genetic variant on chromosome 1, position 1041678, affects the gene AGRN (agrin). Is this variant benign or pathogenic? If pathogenic, what disease(s) does it cause?	pathogenic; ['Congenital_myasthenic_syndrome_8', 'Presynaptic_congenital_myasthenic_syndrome']	GTGCCTGAGGCAGCTTTGTTGGCCACGTTGAGGTCTGGTGATGGGACGTGTGTCAGGCGCTGTGGTCTGCAGCTGTAAGAACTAAAATGAGCAACAGTTCCTGCACCTCTCCAAGAAGGAAGTTCGCTTTGACAGAGAGTGAGGGCGATGGAGGAGGCAAGAGTGAGGTGGGGGGCCGGGGGATGCCCAGGGAGGAGGGGGCGTGTGGGTGCCCCAGGGATCCCAGGGAGCGATGGGAGGCTGCAGAAGGGCACAGGCCTGCCGCGGGTGGGGGGCTGGCCAGGGAGAATAGGAGATAGTAGAGGCGGAGGCCAGGAATT...	GTGCCTGAGGCAGCTTTGTTGGCCACGTTGAGGTCTGGTGATGGGACGTGTGTCAGGCGCTGTGGTCTGCAGCTGTAAGAACTAAAATGAGCAACAGTTCCTGCACCTCTCCAAGAAGGAAGTTCGCTTTGACAGAGAGTGAGGGCGATGGAGGAGGCAAGAGTGAGGTGGGGGGCCGGGGGATGCCCAGGGAGGAGGGGGCGTGTGGGTGCCCCAGGGATCCCAGGGAGCGATGGGAGGCTGCAGAAGGGCACAGGCCTGCCGCGGGTGGGGGGCTGGCCAGGGAGAATAGGAGATAGTAGAGGCGGAGGCCAGGAATT...	pathogenic	80
A genetic variant at chromosome 1, position 1043223, affecting gene AGRN (agrin)—is it benign or pathogenic? If pathogenic, identify the associated disorder(s).	benign	TCGCGGGACCCCTGCTCCAACGTGACCTGCAGCTTCGGCAGCACCTGTGCGCGCTCGGCCGACGGGCTGACGGCCTCGTGCCTGTGCCCCGCGACCTGCCGTGGCGCCCCCGAGGGGACCGTCTGCGGCAGCGACGGCGCCGACTACCCCGGCGAGTGCCAGCTCCTGCGCCGCGCCTGCGCCCGCCAGGAGAATGTCTTCAAGAAGTTCGACGGCCCTTGTGGTGAGCGCGGCGGCGGGCGCACGGCTCGAGCTCTGTGGGCGCGCGGCGACAGCGTCCTGACTCCTGCCCTCGACCCCCAGACCCCTGTCAGGGCGCC...	TCGCGGGACCCCTGCTCCAACGTGACCTGCAGCTTCGGCAGCACCTGTGCGCGCTCGGCCGACGGGCTGACGGCCTCGTGCCTGTGCCCCGCGACCTGCCGTGGCGCCCCCGAGGGGACCGTCTGCGGCAGCGACGGCGCCGACTACCCCGGCGAGTGCCAGCTCCTGCGCCGCGCCTGCGCCCGCCAGGAGAATGTCTTCAAGAAGTTCGACGGCCCTTGTGGTGAGCGCGGCGGCGGGCGCACGGCTCGAGCTCTGTGGGCGCGCGGCGACAGCGTCCTGACTCCTGCCCTCGACCCCCAGACCCCTGTCAGGGCGCC...	benign	90
Clinical classification of chromosome 1, position 1048791, gene AGRN (agrin): benign or pathogenic? Disease(s) if pathogenic?	benign	GGGATCAAGGACTTGGGGTGGGTGGGCAGGCGCCGAGAGGCTCCACCAGAGCCTGGGCTCAGAGCGCGTCTCCCCAGGGCTCGAGCCCTTGGAGGGCAGCAGCGTGGCCACCCCTGGGCCACCTGTCGAGAGGGCTTCCTGCTACAACTCCGCGTTGGGCTGCTGCTCTGATGGGAAGACGCCCTCGCTGGACGCAGAGGGCTCCAACTGCCCCGGTGAGTGGACGGCTGGGCGAGGGGAGTGTGAGGATAGCCTGGGCTCGGCCGAGGTGCTGCCCCCTCGCCTGGGCAGCAGGTCAGTGCCGGGGGTTATGGTCTTGG...	GGGATCAAGGACTTGGGGTGGGTGGGCAGGCGCCGAGAGGCTCCACCAGAGCCTGGGCTCAGAGCGCGTCTCCCCAGGGCTCGAGCCCTTGGAGGGCAGCAGCGTGGCCACCCCTGGGCCACCTGTCGAGAGGGCTTCCTGCTACAACTCCGCGTTGGGCTGCTGCTCTGATGGGAAGACGCCCTCGCTGGACGCAGAGGGCTCCAACTGCCCCGGTGAGTGGACGGCTGGGCGAGGGGAGTGTGAGGATAGCCTGGGCTCGGCCGAGGTGCTGCCCCCTCGCCTGGGCAGCAGGTCAGTGCCGGGGGTTATGGTCTTGG...	benign	166
Gene AGRN (agrin) variant at chromosome 1, position 1048977—is it benign or pathogenic? If pathogenic, what are the associated condition(s)?	pathogenic; ['Congenital_myasthenic_syndrome_8']	GCTGGACGCAGAGGGCTCCAACTGCCCCGGTGAGTGGACGGCTGGGCGAGGGGAGTGTGAGGATAGCCTGGGCTCGGCCGAGGTGCTGCCCCCTCGCCTGGGCAGCAGGTCAGTGCCGGGGGTTATGGTCTTGGGACTCGGCCCCCTCAAACATGTGCGTGCCGGGGACCCCACGCCTAACCCGTCTCTCTCGTTGCAAGCCGGTGTGGCACACTGCTCTGAGGAGTCCTCCTGGTAACCGACACCAGCCCCACCCTGGGGTCCCCACTAACCTCATGACCATCTGACTAACATCCACCTTCCCTTGCACCCTTGTGGCT...	GCTGGACGCAGAGGGCTCCAACTGCCCCGGTGAGTGGACGGCTGGGCGAGGGGAGTGTGAGGATAGCCTGGGCTCGGCCGAGGTGCTGCCCCCTCGCCTGGGCAGCAGGTCAGTGCCGGGGGTTATGGTCTTGGGACTCGGCCCCCTCAAACATGTGCGTGCCGGGGACCCCACGCCTAACCCGTCTCTCTCGTTGCAAGCCGGTGTGGCACACTGCTCTGAGGAGTCCTCCTGGTAACCGACACCAGCCCCACCCTGGGGTCCCCACTAACCTCATGACCATCTGACTAACATCCACCTTCCCTTGCACCCTTGTGGCT...	pathogenic	172
Does the variant impacting DVL1 (dishevelled segment polarity protein 1) on chromosome 1, position 1338096, classify as benign or pathogenic? If pathogenic, what disease(s) is it associated with?	pathogenic; ['Autosomal_dominant_Robinow_syndrome_2']	TCCTGGCCCCCACGAAGGCAAGCCCACGCGAGCTCTGCATGCGGCAGGACCGCCAGCTCCCCACCTCAGGCAGGGCTGGGGCATGCGCCACGAGTCACATGATGTCCACGAAGAACTCGCAGGGGTTCCCCATAGCCTTCTGGAAGGACTGGCGGCTGCCTGTCAATTCCGGGGGGACGGCAGCCAGCTCCCGGACAGGGGGTCCCCCGGGTGGCCCCCCCACCACTGTATAGGCCTTGGTCGTGGGGTGGGGCGGGGGGAGCCCCGGGGCGGTAGCCGAGGCCTGACTGCGTGGGCTGCTGCCACGGCTGAGCTGGCCG...	TCCTGGCCCCCACGAAGGCAAGCCCACGCGAGCTCTGCATGCGGCAGGACCGCCAGCTCCCCACCTCAGGCAGGGCTGGGGCATGCGCCACGAGTCACATGATGTCCACGAAGAACTCGCAGGGGTTCCCCATAGCCTTCTGGAAGGACTGGCGGCTGCCTGTCAATTCCGGGGGGACGGCAGCCAGCTCCCGGACAGGGGGTCCCCCGGGTGGCCCCCCCACCACTGTATAGGCCTTGGTCGTGGGGTGGGGCGGGGGGAGCCCCGGGGCGGTAGCCGAGGCCTGACTGCGTGGGCTGCTGCCACGGCTGAGCTGGCCG...	pathogenic	327
Clinical impact (benign or pathogenic) of the variant at chromosome 1, location 1338107, gene DVL1 (dishevelled segment polarity protein 1): what disease(s) if pathogenic?	pathogenic; ['Autosomal_dominant_Robinow_syndrome_2']	ACGAAGGCAAGCCCACGCGAGCTCTGCATGCGGCAGGACCGCCAGCTCCCCACCTCAGGCAGGGCTGGGGCATGCGCCACGAGTCACATGATGTCCACGAAGAACTCGCAGGGGTTCCCCATAGCCTTCTGGAAGGACTGGCGGCTGCCTGTCAATTCCGGGGGGACGGCAGCCAGCTCCCGGACAGGGGGTCCCCCGGGTGGCCCCCCCACCACTGTATAGGCCTTGGTCGTGGGGTGGGGCGGGGGGAGCCCCGGGGCGGTAGCCGAGGCCTGACTGCGTGGGCTGCTGCCACGGCTGAGCTGGCCGGCCGGACGCTC...	ACGAAGGCAAGCCCACGCGAGCTCTGCATGCGGCAGGACCGCCAGCTCCCCACCTCAGGCAGGGCTGGGGCATGCGCCACGAGTCACATGATGTCCACGAAGAACTCGCAGGGGTTCCCCATAGCCTTCTGGAAGGACTGGCGGCTGCCTGTCAATTCCGGGGGGACGGCAGCCAGCTCCCGGACAGGGGGTCCCCCGGGTGGCCCCCCCACCACTGTATAGGCCTTGGTCGTGGGGTGGGGCGGGGGGAGCCCCGGGGCGGTAGCCGAGGCCTGACTGCGTGGGCTGCTGCCACGGCTGAGCTGGCCGGCCGGACGCTC...	pathogenic	328
Gene DVL1 (dishevelled segment polarity protein 1) variant at chromosome 1, position 1341593—is it benign or pathogenic? If pathogenic, what are the associated condition(s)?	benign	TCCCCATCCCGCCCCGTGTGCCCCGAGGGCCACTCACCCCGTGGGACGGTGAAGTAGCTTCGGGGCGTTGGGTCCCAGCACTTGGCCACAGTGAGGCTGATGGGCCTGCAGGAACGGTGGTCACACAGCAAGGCCCCCATGGTCCCACCTCCCTGCCTGGCCCCTCCCGCTCCAGCGCCCCCAGCCCTCACCCCGTCTGGGAAACGATCTCCCGCAGCACCCGCACGGCATCGTCATTGCTCATGTTCTCAAAGTTCACGTCATTCACCTGCAGGGGTGGGGATTAGGGTGGTGCAGGCAGGATGTGCAGCTCAGTCCAC...	TCCCCATCCCGCCCCGTGTGCCCCGAGGGCCACTCACCCCGTGGGACGGTGAAGTAGCTTCGGGGCGTTGGGTCCCAGCACTTGGCCACAGTGAGGCTGATGGGCCTGCAGGAACGGTGGTCACACAGCAAGGCCCCCATGGTCCCACCTCCCTGCCTGGCCCCTCCCGCTCCAGCGCCCCCAGCCCTCACCCCGTCTGGGAAACGATCTCCCGCAGCACCCGCACGGCATCGTCATTGCTCATGTTCTCAAAGTTCACGTCATTCACCTGCAGGGGTGGGGATTAGGGTGGTGCAGGCAGGATGTGCAGCTCAGTCCAC...	benign	354
Is the chromosome 1, position 1341659 variant in DVL1 (dishevelled segment polarity protein 1) clinically benign or pathogenic? If pathogenic, what condition(s) is associated?	benign	GTTGGGTCCCAGCACTTGGCCACAGTGAGGCTGATGGGCCTGCAGGAACGGTGGTCACACAGCAAGGCCCCCATGGTCCCACCTCCCTGCCTGGCCCCTCCCGCTCCAGCGCCCCCAGCCCTCACCCCGTCTGGGAAACGATCTCCCGCAGCACCCGCACGGCATCGTCATTGCTCATGTTCTCAAAGTTCACGTCATTCACCTGCAGGGGTGGGGATTAGGGTGGTGCAGGCAGGATGTGCAGCTCAGTCCACCGCCCCCGCAGACCCACCCACAGCCGCATGTCCCCCAGCAGCCCCCGCAGACCCACCCGCAGCCGC...	GTTGGGTCCCAGCACTTGGCCACAGTGAGGCTGATGGGCCTGCAGGAACGGTGGTCACACAGCAAGGCCCCCATGGTCCCACCTCCCTGCCTGGCCCCTCCCGCTCCAGCGCCCCCAGCCCTCACCCCGTCTGGGAAACGATCTCCCGCAGCACCCGCACGGCATCGTCATTGCTCATGTTCTCAAAGTTCACGTCATTCACCTGCAGGGGTGGGGATTAGGGTGGTGCAGGCAGGATGTGCAGCTCAGTCCACCGCCCCCGCAGACCCACCCACAGCCGCATGTCCCCCAGCAGCCCCCGCAGACCCACCCGCAGCCGC...	benign	355
Clinical classification of chromosome 1, position 1435798, gene VWA1 (von Willebrand factor A domain containing 1): benign or pathogenic? Disease(s) if pathogenic?	pathogenic; ['Neuromuscular_disease', 'Neuronopathy,_distal_hereditary_motor,_autosomal_recessive_7', 'VWA1-related_disorder']	CCACGTCCCTCCTCCGGGGTGGAGACAGCGGGGGGAGGGCAGGACACAAGAATGAGTCCTGAAGACTGAGGGGCACGGGGAGAGCTGATGGGGAGGGTCTCCTAGCTGGAGGGACTCCAGGCAGAGCCGGGAGCAAGGCAGGTGGCTGAGCTCGGCCCAGGCTGGGTGGAGGCCAGGCCTCCTGTGCCTTCTCCCGCTGATGGCGAGCTGAAGGGAGGAGGGCGGCCGCTTCCTTGAGGGCCTGAGTCACAGCCAAGAAGACCCGCTCACTTTTTCCAGAAGTGAGGGAAACTTCCCCGTCAGCCCTGCAAGGCTGGCTG...	CCACGTCCCTCCTCCGGGGTGGAGACAGCGGGGGGAGGGCAGGACACAAGAATGAGTCCTGAAGACTGAGGGGCACGGGGAGAGCTGATGGGGAGGGTCTCCTAGCTGGAGGGACTCCAGGCAGAGCCGGGAGCAAGGCAGGTGGCTGAGCTCGGCCCAGGCTGGGTGGAGGCCAGGCCTCCTGTGCCTTCTCCCGCTGATGGCGAGCTGAAGGGAGGAGGGCGGCCGCTTCCTTGAGGGCCTGAGTCACAGCCAAGAAGACCCGCTCACTTTTTCCAGAAGTGAGGGAAACTTCCCCGTCAGCCCTGCAAGGCTGGCTG...	pathogenic	369
Mutation found at chromosome 1 position 1437308, gene VWA1 (von Willebrand factor A domain containing 1): benign or pathogenic? If pathogenic, indicate the relevant disease(s).	pathogenic; ['Neuronopathy,_distal_hereditary_motor,_autosomal_recessive_7']	TCTGGACGTGTTTTTTTGGTGCCACCGCCAGCCCCTGGGGTTCTCTTGGGCCTGGCTGCTGGGACCCCAGCACCCAGAGTCACGGCAGTGGTGGGCATGGGGAGGGCCTAGCCTGGTACCTCCCTGCTCGGCTCCCGCGGCTGGGGGTCGGAGAGGGGTGGAGAGCGTGGGCCGCACAGCCTCGGCCGGGAGAGGGAGACTGGAGTGTGTGTGTGTGCGTGCCTGCGCGTGCGTGCCTCGGTCGTATCTCGGCTGGTGCTGCGTGTCCCTGCGTGTCGGGGTCCGCTCGTGCGCGCCTCTCCGGGGTCTGTGCGCGTGGC...	TCTGGACGTGTTTTTTTGGTGCCACCGCCAGCCCCTGGGGTTCTCTTGGGCCTGGCTGCTGGGACCCCAGCACCCAGAGTCACGGCAGTGGTGGGCATGGGGAGGGCCTAGCCTGGTACCTCCCTGCTCGGCTCCCGCGGCTGGGGGTCGGAGAGGGGTGGAGAGCGTGGGCCGCACAGCCTCGGCCGGGAGAGGGAGACTGGAGTGTGTGTGTGTGCGTGCCTGCGCGTGCGTGCCTCGGTCGTATCTCGGCTGGTGCTGCGTGTCCCTGCGTGTCGGGGTCCGCTCGTGCGCGCCTCTCCGGGGTCTGTGCGCGTGGC...	pathogenic	371
Is chromosome 1, position 1439536, gene VWA1 (von Willebrand factor A domain containing 1) variant benign or pathogenic? If pathogenic, what condition(s) is it related to?	pathogenic; ['Neuronopathy,_distal_hereditary_motor,_autosomal_recessive_7']	TGCGGGAGGAGGCAGGGCCCAGGGAGCCCTAGCTGGGAGCCGCAGAAGGAGAGGCTGGGTTGAGACTTTGGGAAGATCTCATGTCCCCAGAGCAGCGGCCAGGGCCTCCGGGGCTGTGGTACCCCTAGGGTGCAGGGCTGAGTGATGCAGCTTGTCTATGCACACTCTTCACTGGGCGACCCGTGTACCCTGCTGAGACGGGGGCAGGCTTGAGTAGCCACCTCCAGGTGTAGCTCCCTGCTGATGTGTCCAGCCCAGACCTCGAGGCCCCAGGGAGTGCAGAGCCCGGGTGTAGGCCCAGGAAGAAGCTTCCAAGTCTG...	TGCGGGAGGAGGCAGGGCCCAGGGAGCCCTAGCTGGGAGCCGCAGAAGGAGAGGCTGGGTTGAGACTTTGGGAAGATCTCATGTCCCCAGAGCAGCGGCCAGGGCCTCCGGGGCTGTGGTACCCCTAGGGTGCAGGGCTGAGTGATGCAGCTTGTCTATGCACACTCTTCACTGGGCGACCCGTGTACCCTGCTGAGACGGGGGCAGGCTTGAGTAGCCACCTCCAGGTGTAGCTCCCTGCTGATGTGTCCAGCCCAGACCTCGAGGCCCCAGGGAGTGCAGAGCCCGGGTGTAGGCCCAGGAAGAAGCTTCCAAGTCTG...	pathogenic	377
The chromosome 1, position 2406525 genetic variant in gene PEX10 (peroxisomal biogenesis factor 10): benign or pathogenic? If pathogenic, indicate disease(s).	pathogenic; ['Peroxisome_biogenesis_disorder,_complementation_group_7', 'Peroxisome_biogenesis_disorder_6A_(Zellweger)']	AAAGGACTGGGTGCTGATGGATGGAGCCACGGCGGCATCTGCCCACCCGGCCGCAGCCCCCAGTGCCTCTCCTGGTGGTCCTCCCAGTCTAGAGGGTCACGGCCCCCCCGCCCTCCTCCGTCTCTGGCAAGCTGACCTTGACTAACCCAGGAATACAGGGTCATCCTCATTCCTAAGTAAGTCAAACAGCAAGACATGGTTTGCGCGGGTCTTTGCCGGAAGCCGGTCCTGCTGGCCAGGTGTTTTACGTCAGCAGGGAAATGTGGCACACGCCCTCGAGGCATTTTAACACTGCGCTTCAGGAAATCTCAAGTTCCATC...	AAAGGACTGGGTGCTGATGGATGGAGCCACGGCGGCATCTGCCCACCCGGCCGCAGCCCCCAGTGCCTCTCCTGGTGGTCCTCCCAGTCTAGAGGGTCACGGCCCCCCCGCCCTCCTCCGTCTCTGGCAAGCTGACCTTGACTAACCCAGGAATACAGGGTCATCCTCATTCCTAAGTAAGTCAAACAGCAAGACATGGTTTGCGCGGGTCTTTGCCGGAAGCCGGTCCTGCTGGCCAGGTGTTTTACGTCAGCAGGGAAATGTGGCACACGCCCTCGAGGCATTTTAACACTGCGCTTCAGGAAATCTCAAGTTCCATC...	pathogenic	758
Classify the chromosome 1 variant at position 2406527 affecting gene PEX10 (peroxisomal biogenesis factor 10) as benign or pathogenic. If pathogenic, which disease(s) is associated?	pathogenic; ['Peroxisome_biogenesis_disorder', 'Peroxisome_biogenesis_disorder,_complementation_group_7']	AGGACTGGGTGCTGATGGATGGAGCCACGGCGGCATCTGCCCACCCGGCCGCAGCCCCCAGTGCCTCTCCTGGTGGTCCTCCCAGTCTAGAGGGTCACGGCCCCCCCGCCCTCCTCCGTCTCTGGCAAGCTGACCTTGACTAACCCAGGAATACAGGGTCATCCTCATTCCTAAGTAAGTCAAACAGCAAGACATGGTTTGCGCGGGTCTTTGCCGGAAGCCGGTCCTGCTGGCCAGGTGTTTTACGTCAGCAGGGAAATGTGGCACACGCCCTCGAGGCATTTTAACACTGCGCTTCAGGAAATCTCAAGTTCCATCTT...	AGGACTGGGTGCTGATGGATGGAGCCACGGCGGCATCTGCCCACCCGGCCGCAGCCCCCAGTGCCTCTCCTGGTGGTCCTCCCAGTCTAGAGGGTCACGGCCCCCCCGCCCTCCTCCGTCTCTGGCAAGCTGACCTTGACTAACCCAGGAATACAGGGTCATCCTCATTCCTAAGTAAGTCAAACAGCAAGACATGGTTTGCGCGGGTCTTTGCCGGAAGCCGGTCCTGCTGGCCAGGTGTTTTACGTCAGCAGGGAAATGTGGCACACGCCCTCGAGGCATTTTAACACTGCGCTTCAGGAAATCTCAAGTTCCATCTT...	pathogenic	759
Variant at chromosome position 2406580, chromosome 1, gene PEX10 (peroxisomal biogenesis factor 10): benign or pathogenic? If pathogenic, what condition(s) does it relate to?	pathogenic; ['Peroxisome_biogenesis_disorder', 'Peroxisome_biogenesis_disorder,_complementation_group_7', 'Peroxisome_biogenesis_disorder_6A_(Zellweger)', 'Peroxisome_biogenesis_disorder_6B', 'Zellweger_spectrum_disorders']	GCCCCCAGTGCCTCTCCTGGTGGTCCTCCCAGTCTAGAGGGTCACGGCCCCCCCGCCCTCCTCCGTCTCTGGCAAGCTGACCTTGACTAACCCAGGAATACAGGGTCATCCTCATTCCTAAGTAAGTCAAACAGCAAGACATGGTTTGCGCGGGTCTTTGCCGGAAGCCGGTCCTGCTGGCCAGGTGTTTTACGTCAGCAGGGAAATGTGGCACACGCCCTCGAGGCATTTTAACACTGCGCTTCAGGAAATCTCAAGTTCCATCTTGTGTTAGTAACGTACCCACATTTTGCTGGAGTTAGTTTATTAAAGATGCCTAC...	GCCCCCAGTGCCTCTCCTGGTGGTCCTCCCAGTCTAGAGGGTCACGGCCCCCCCGCCCTCCTCCGTCTCTGGCAAGCTGACCTTGACTAACCCAGGAATACAGGGTCATCCTCATTCCTAAGTAAGTCAAACAGCAAGACATGGTTTGCGCGGGTCTTTGCCGGAAGCCGGTCCTGCTGGCCAGGTGTTTTACGTCAGCAGGGAAATGTGGCACACGCCCTCGAGGCATTTTAACACTGCGCTTCAGGAAATCTCAAGTTCCATCTTGTGTTAGTAACGTACCCACATTTTGCTGGAGTTAGTTTATTAAAGATGCCTAC...	pathogenic	764
Considering the variant on chromosome 1, location 2406599, involving gene PEX10 (peroxisomal biogenesis factor 10), would you classify it as benign or pathogenic? What disease(s), if any, does a pathogenic variant indicate?	pathogenic; ['Peroxisome_biogenesis_disorder,_complementation_group_7', 'Peroxisome_biogenesis_disorder_6A_(Zellweger)', 'Peroxisome_biogenesis_disorder_6B']	GTGGTCCTCCCAGTCTAGAGGGTCACGGCCCCCCCGCCCTCCTCCGTCTCTGGCAAGCTGACCTTGACTAACCCAGGAATACAGGGTCATCCTCATTCCTAAGTAAGTCAAACAGCAAGACATGGTTTGCGCGGGTCTTTGCCGGAAGCCGGTCCTGCTGGCCAGGTGTTTTACGTCAGCAGGGAAATGTGGCACACGCCCTCGAGGCATTTTAACACTGCGCTTCAGGAAATCTCAAGTTCCATCTTGTGTTAGTAACGTACCCACATTTTGCTGGAGTTAGTTTATTAAAGATGCCTACGGTGAACTCTCTGGCGCAG...	GTGGTCCTCCCAGTCTAGAGGGTCACGGCCCCCCCGCCCTCCTCCGTCTCTGGCAAGCTGACCTTGACTAACCCAGGAATACAGGGTCATCCTCATTCCTAAGTAAGTCAAACAGCAAGACATGGTTTGCGCGGGTCTTTGCCGGAAGCCGGTCCTGCTGGCCAGGTGTTTTACGTCAGCAGGGAAATGTGGCACACGCCCTCGAGGCATTTTAACACTGCGCTTCAGGAAATCTCAAGTTCCATCTTGTGTTAGTAACGTACCCACATTTTGCTGGAGTTAGTTTATTAAAGATGCCTACGGTGAACTCTCTGGCGCAG...	pathogenic	765
Is chromosome 1, position 2406734, gene PEX10 (peroxisomal biogenesis factor 10) variant benign or pathogenic? If pathogenic, what condition(s) is it related to?	pathogenic; ['Peroxisome_biogenesis_disorder,_complementation_group_7', 'Peroxisome_biogenesis_disorder_6A_(Zellweger)', 'Peroxisome_biogenesis_disorder_6B']	TCTTTGCCGGAAGCCGGTCCTGCTGGCCAGGTGTTTTACGTCAGCAGGGAAATGTGGCACACGCCCTCGAGGCATTTTAACACTGCGCTTCAGGAAATCTCAAGTTCCATCTTGTGTTAGTAACGTACCCACATTTTGCTGGAGTTAGTTTATTAAAGATGCCTACGGTGAACTCTCTGGCGCAGGTTAAATGCAGTTTTGAAAACCTGGAAACATCAAATGGAGGCGGGAAATAGGCTGGGGCCGAGCTGAGGGGCTGAACACAGCAGTGACCGTGGGTCAGCAGGTCGCCTGCCCAGCAGGCCCCCCAGGAGAGGGCT...	TCTTTGCCGGAAGCCGGTCCTGCTGGCCAGGTGTTTTACGTCAGCAGGGAAATGTGGCACACGCCCTCGAGGCATTTTAACACTGCGCTTCAGGAAATCTCAAGTTCCATCTTGTGTTAGTAACGTACCCACATTTTGCTGGAGTTAGTTTATTAAAGATGCCTACGGTGAACTCTCTGGCGCAGGTTAAATGCAGTTTTGAAAACCTGGAAACATCAAATGGAGGCGGGAAATAGGCTGGGGCCGAGCTGAGGGGCTGAACACAGCAGTGACCGTGGGTCAGCAGGTCGCCTGCCCAGCAGGCCCCCCAGGAGAGGGCT...	pathogenic	771
Gene PEX10 (peroxisomal biogenesis factor 10) variant at chromosome 1, position 2406739—is it benign or pathogenic? If pathogenic, what are the associated condition(s)?	pathogenic; ['Peroxisome_biogenesis_disorder,_complementation_group_7', 'Peroxisome_biogenesis_disorder_6A_(Zellweger)', 'Peroxisome_biogenesis_disorder_6B']	GCCGGAAGCCGGTCCTGCTGGCCAGGTGTTTTACGTCAGCAGGGAAATGTGGCACACGCCCTCGAGGCATTTTAACACTGCGCTTCAGGAAATCTCAAGTTCCATCTTGTGTTAGTAACGTACCCACATTTTGCTGGAGTTAGTTTATTAAAGATGCCTACGGTGAACTCTCTGGCGCAGGTTAAATGCAGTTTTGAAAACCTGGAAACATCAAATGGAGGCGGGAAATAGGCTGGGGCCGAGCTGAGGGGCTGAACACAGCAGTGACCGTGGGTCAGCAGGTCGCCTGCCCAGCAGGCCCCCCAGGAGAGGGCTCGGGC...	GCCGGAAGCCGGTCCTGCTGGCCAGGTGTTTTACGTCAGCAGGGAAATGTGGCACACGCCCTCGAGGCATTTTAACACTGCGCTTCAGGAAATCTCAAGTTCCATCTTGTGTTAGTAACGTACCCACATTTTGCTGGAGTTAGTTTATTAAAGATGCCTACGGTGAACTCTCTGGCGCAGGTTAAATGCAGTTTTGAAAACCTGGAAACATCAAATGGAGGCGGGAAATAGGCTGGGGCCGAGCTGAGGGGCTGAACACAGCAGTGACCGTGGGTCAGCAGGTCGCCTGCCCAGCAGGCCCCCCAGGAGAGGGCTCGGGC...	pathogenic	772
Regarding the variant found on chromosome 1 at position 2406791 in gene PEX10 (peroxisomal biogenesis factor 10): is it benign or pathogenic? If pathogenic, identify the disease(s).	pathogenic; ['PEX10-related_disorder', 'Peroxisome_biogenesis_disorder', 'Peroxisome_biogenesis_disorder,_complementation_group_7', 'Peroxisome_biogenesis_disorder_6A_(Zellweger)', 'Peroxisome_biogenesis_disorder_6B', 'Zellweger_spectrum_disorders']	CACACGCCCTCGAGGCATTTTAACACTGCGCTTCAGGAAATCTCAAGTTCCATCTTGTGTTAGTAACGTACCCACATTTTGCTGGAGTTAGTTTATTAAAGATGCCTACGGTGAACTCTCTGGCGCAGGTTAAATGCAGTTTTGAAAACCTGGAAACATCAAATGGAGGCGGGAAATAGGCTGGGGCCGAGCTGAGGGGCTGAACACAGCAGTGACCGTGGGTCAGCAGGTCGCCTGCCCAGCAGGCCCCCCAGGAGAGGGCTCGGGCGCCCCTGGCAGCCCCCATACCCCCAGGACCTGGCTCGTGAGTGCGTCTGGGT...	CACACGCCCTCGAGGCATTTTAACACTGCGCTTCAGGAAATCTCAAGTTCCATCTTGTGTTAGTAACGTACCCACATTTTGCTGGAGTTAGTTTATTAAAGATGCCTACGGTGAACTCTCTGGCGCAGGTTAAATGCAGTTTTGAAAACCTGGAAACATCAAATGGAGGCGGGAAATAGGCTGGGGCCGAGCTGAGGGGCTGAACACAGCAGTGACCGTGGGTCAGCAGGTCGCCTGCCCAGCAGGCCCCCCAGGAGAGGGCTCGGGCGCCCCTGGCAGCCCCCATACCCCCAGGACCTGGCTCGTGAGTGCGTCTGGGT...	pathogenic	775
Is the genetic variant on chromosome 1, position 2406792, gene PEX10 (peroxisomal biogenesis factor 10), benign or pathogenic? If pathogenic, what disease(s) is indicated?	pathogenic; ['Peroxisome_biogenesis_disorder,_complementation_group_7', 'Peroxisome_biogenesis_disorder_6A_(Zellweger)', 'Peroxisome_biogenesis_disorder_6B']	ACACGCCCTCGAGGCATTTTAACACTGCGCTTCAGGAAATCTCAAGTTCCATCTTGTGTTAGTAACGTACCCACATTTTGCTGGAGTTAGTTTATTAAAGATGCCTACGGTGAACTCTCTGGCGCAGGTTAAATGCAGTTTTGAAAACCTGGAAACATCAAATGGAGGCGGGAAATAGGCTGGGGCCGAGCTGAGGGGCTGAACACAGCAGTGACCGTGGGTCAGCAGGTCGCCTGCCCAGCAGGCCCCCCAGGAGAGGGCTCGGGCGCCCCTGGCAGCCCCCATACCCCCAGGACCTGGCTCGTGAGTGCGTCTGGGTC...	ACACGCCCTCGAGGCATTTTAACACTGCGCTTCAGGAAATCTCAAGTTCCATCTTGTGTTAGTAACGTACCCACATTTTGCTGGAGTTAGTTTATTAAAGATGCCTACGGTGAACTCTCTGGCGCAGGTTAAATGCAGTTTTGAAAACCTGGAAACATCAAATGGAGGCGGGAAATAGGCTGGGGCCGAGCTGAGGGGCTGAACACAGCAGTGACCGTGGGTCAGCAGGTCGCCTGCCCAGCAGGCCCCCCAGGAGAGGGCTCGGGCGCCCCTGGCAGCCCCCATACCCCCAGGACCTGGCTCGTGAGTGCGTCTGGGTC...	pathogenic	776
A genetic variant at chromosome 1, position 2406931, affecting gene PEX10 (peroxisomal biogenesis factor 10)—is it benign or pathogenic? If pathogenic, identify the associated disorder(s).	pathogenic; ['Peroxisome_biogenesis_disorder,_complementation_group_7', 'Peroxisome_biogenesis_disorder_6A_(Zellweger)', 'Peroxisome_biogenesis_disorder_6B']	TTTGAAAACCTGGAAACATCAAATGGAGGCGGGAAATAGGCTGGGGCCGAGCTGAGGGGCTGAACACAGCAGTGACCGTGGGTCAGCAGGTCGCCTGCCCAGCAGGCCCCCCAGGAGAGGGCTCGGGCGCCCCTGGCAGCCCCCATACCCCCAGGACCTGGCTCGTGAGTGCGTCTGGGTCAGGAAGAGACCTCTCTGTGCGTCTCAGGCTGAGATGCAGATTTCTGTTTTCTAAAACTGGAAGCGACCTTGACGTGTATTGAAGGTGTGTGTGCCAAATGCTTCCGACGGAGGTGCTGGCCTTGGTTGGTTTCTCTCTG...	TTTGAAAACCTGGAAACATCAAATGGAGGCGGGAAATAGGCTGGGGCCGAGCTGAGGGGCTGAACACAGCAGTGACCGTGGGTCAGCAGGTCGCCTGCCCAGCAGGCCCCCCAGGAGAGGGCTCGGGCGCCCCTGGCAGCCCCCATACCCCCAGGACCTGGCTCGTGAGTGCGTCTGGGTCAGGAAGAGACCTCTCTGTGCGTCTCAGGCTGAGATGCAGATTTCTGTTTTCTAAAACTGGAAGCGACCTTGACGTGTATTGAAGGTGTGTGTGCCAAATGCTTCCGACGGAGGTGCTGGCCTTGGTTGGTTTCTCTCTG...	pathogenic	781
Gene PEX10 (peroxisomal biogenesis factor 10) variant at chromosome 1, position 2408464—is it benign or pathogenic? If pathogenic, what are the associated condition(s)?	pathogenic; ['Peroxisome_biogenesis_disorder', 'Peroxisome_biogenesis_disorder_6A_(Zellweger)']	TGCAGCCAGGTGCATCTTGCCGGCACAGCCGCTGACCACCCCAGGACGGCAGCAGGCTCCCACCTCACCTTGCTGCTGCACCACGCGGTGATGCACTCCCAGCAGAACAGGTGGCCGCAGGGCGTGGCTGTTGGGTGCCTGCGCTCCTCCAGGCACAGGGTGCACAGGGGGTTTCTGGAAACGGCTCTCTCCTCCAAGGAGGCCCTGGGGAAGGTGGGGCAGAGCGTCAAGGTGGGTGCACCTTACAGGTCCTTGTGAAGTGCCCAGGACACCCCCAGCCCCCATGTGTGGCCCCCGCACGCACCTGCGGTGAGACAGGC...	TGCAGCCAGGTGCATCTTGCCGGCACAGCCGCTGACCACCCCAGGACGGCAGCAGGCTCCCACCTCACCTTGCTGCTGCACCACGCGGTGATGCACTCCCAGCAGAACAGGTGGCCGCAGGGCGTGGCTGTTGGGTGCCTGCGCTCCTCCAGGCACAGGGTGCACAGGGGGTTTCTGGAAACGGCTCTCTCCTCCAAGGAGGCCCTGGGGAAGGTGGGGCAGAGCGTCAAGGTGGGTGCACCTTACAGGTCCTTGTGAAGTGCCCAGGACACCCCCAGCCCCCATGTGTGGCCCCCGCACGCACCTGCGGTGAGACAGGC...	pathogenic	785

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🧬 BioReason
Incentivizing Multimodal Biological Reasoning within a DNA-LLM Model

Variant Effect Coding Non-SNVs Dataset

36,088 core non-SNV entries from ClinVar 2024-02-28 release, filtered for coding variants with ≥2-star review status, using stratified train/test splits for balanced disease representation in pathogenic/benign classification.

Usage

from datasets import load_dataset

dataset = load_dataset("wanglab/variant_effect_non_snv")
example = dataset["train"][0]
print(example)

Citation

@misc{fallahpour2025bioreasonincentivizingmultimodalbiological,
      title={BioReason: Incentivizing Multimodal Biological Reasoning within a DNA-LLM Model}, 
      author={Adibvafa Fallahpour and Andrew Magnuson and Purav Gupta and Shihao Ma and Jack Naimer and Arnav Shah and Haonan Duan and Omar Ibrahim and Hani Goodarzi and Chris J. Maddison and Bo Wang},
      year={2025},
      eprint={2505.23579},
      archivePrefix={arXiv},
      primaryClass={cs.LG},
      url={https://arxiv.org/abs/2505.23579}, 
}