GPN-MSA
Collection
https://www.nature.com/articles/s41587-024-02511-w
•
11 items
•
Updated
•
5
chrom
large_stringlengths 1
2
| pos
int64 10.4k
249M
| ref
large_stringlengths 1
1
| alt
large_stringlengths 1
1
| label
bool 2
classes | consequence
large_stringlengths 5
25
| GPN-MSA
float32 -12.11
10.7
| CADD
float32 -8.77
1.95
| phyloP-100v
float64 -9.89
15.7
⌀ | phyloP-241m
float64 -9.19
20
⌀ | phastCons-100v
float64 -1
-0
⌀ | NT
float32 -10.61
9.66
⌀ |
|---|---|---|---|---|---|---|---|---|---|---|---|
1
| 13,273
|
G
|
C
| false
|
ncRNA
| -4.074219
| -0.398596
| -1.091
| -0.864
| -1
| 0.11441
|
1
| 14,464
|
A
|
T
| false
|
ncRNA
| 0.89502
| 0.339809
| 1.705
| -0.992
| -0
| -0.155609
|
1
| 16,688
|
G
|
A
| false
|
ncRNA
| -4.027344
| -1.448712
| -3.121
| -1.305
| -0.996
| -1.57756
|
1
| 17,697
|
G
|
C
| false
|
ncRNA
| -4.734375
| -1.043489
| -2.491
| -8.751
| -1
| 0.863495
|
1
| 49,554
|
A
|
G
| false
|
Enhancer
| -1.988281
| -0.227302
| -0.024
| 0.078
| -0.003
| null |
1
| 51,479
|
T
|
A
| false
|
Promoter
| -1.28125
| -0.208313
| 0.212
| -0.604
| -0.001
| -2.320801
|
1
| 51,803
|
T
|
C
| false
|
Promoter
| -1.322266
| -0.448316
| -0.393
| -0.107
| -0.091
| -3.083298
|
1
| 51,928
|
G
|
A
| false
|
Promoter
| 1.206055
| -0.244843
| -0.176
| 0.06
| -0.001
| 0.418243
|
1
| 52,058
|
G
|
C
| false
|
Promoter
| -1.276367
| 0.07386
| 0.238
| -0.137
| -0
| -0.945038
|
1
| 52,238
|
T
|
G
| false
|
Promoter
| 1.34375
| 0.04854
| 1.025
| -0.078
| -0
| 1.140945
|
1
| 54,366
|
A
|
G
| false
|
Enhancer
| -1.580078
| -0.252664
| -0.289
| -0.107
| -0.067
| null |
1
| 54,380
|
T
|
C
| false
|
Enhancer
| -1.324219
| -0.529307
| 0.018
| 0.162
| -0
| null |
1
| 54,421
|
A
|
G
| false
|
Enhancer
| 1.257813
| -0.02868
| 0.568
| -0.333
| -0.001
| null |
1
| 54,490
|
G
|
A
| false
|
Enhancer
| 0.039063
| 0.201295
| 0.313
| -0.029
| -0
| null |
1
| 54,586
|
T
|
C
| false
|
Enhancer
| 0.9375
| -0.178471
| 0.549
| 0.213
| -0
| null |
1
| 54,676
|
C
|
T
| false
|
Enhancer
| 3.912109
| -0.059604
| 0.086
| -0.285
| -0.007
| null |
1
| 54,844
|
G
|
A
| false
|
Enhancer
| -1.818359
| -0.160976
| -0.514
| -0.527
| -0.004
| null |
1
| 55,164
|
C
|
A
| false
|
Enhancer
| 1.34375
| 0.538769
| 2.152
| 1.826
| -0
| null |
1
| 55,545
|
C
|
T
| false
|
Enhancer
| 1.870117
| -0.295491
| -0.696
| 0.768
| -0.007
| null |
1
| 55,926
|
T
|
C
| false
|
Enhancer
| -1.318359
| 0.20604
| 0.999
| 0.271
| -0
| null |
1
| 58,771
|
T
|
C
| false
|
ncRNA
| -5.105469
| -1.633646
| -1.161
| -0.426
| -0.797
| -1.934265
|
1
| 63,268
|
T
|
C
| false
|
ncRNA
| -2.367188
| 0.038139
| -0.486
| -0.436
| -0
| -3.040726
|
1
| 63,516
|
A
|
G
| false
|
ncRNA
| -2.964844
| -1.075005
| -0.029
| 0.093
| -0
| -2.457718
|
1
| 63,527
|
T
|
C
| false
|
ncRNA
| 0.306152
| -0.163349
| 1.32
| -0.619
| -0
| -1.642197
|
1
| 63,671
|
G
|
A
| false
|
ncRNA
| 3.130859
| -0.344458
| 1.392
| -0.253
| -0
| 2.005463
|
1
| 63,697
|
T
|
C
| false
|
ncRNA
| -6.382813
| -1.180623
| -1.155
| -2.212
| -0.701
| -4.765289
|
1
| 64,025
|
T
|
C
| false
|
ncRNA
| -1.170898
| -0.398742
| -0.081
| -0.51
| -0
| -0.320374
|
1
| 64,764
|
C
|
T
| false
|
Promoter
| 1.634766
| -0.268436
| -0.249
| -0.404
| -0
| 3.997162
|
1
| 64,931
|
G
|
A
| false
|
Promoter
| -0.954102
| -0.062455
| 0.527
| 1.044
| -0
| 1.722168
|
1
| 73,649
|
C
|
G
| false
|
Enhancer
| -2.121094
| -0.451789
| -0.264
| 0.267
| -0.316
| null |
1
| 75,767
|
G
|
A
| false
|
Enhancer
| 0.196289
| -0.115283
| null | -0.086
| null | null |
1
| 76,057
|
A
|
G
| false
|
Enhancer
| -2.160156
| -0.248493
| null | -0.071
| null | null |
1
| 76,206
|
T
|
C
| false
|
Enhancer
| -0.300293
| -0.244829
| null | -0.072
| null | null |
1
| 76,240
|
A
|
G
| false
|
Enhancer
| -0.107422
| -0.269503
| null | -0.071
| null | null |
1
| 76,838
|
T
|
G
| false
|
Enhancer
| -0.165527
| -0.107129
| 1.366
| 1.26
| -0.02
| null |
1
| 76,854
|
A
|
G
| false
|
Enhancer
| 0.055176
| -0.489965
| -0.153
| -0.399
| -0.053
| null |
1
| 77,089
|
C
|
T
| false
|
Enhancer
| 1.47168
| -0.415083
| -0.136
| 0.304
| -0.05
| null |
1
| 77,866
|
C
|
T
| false
|
Enhancer
| 0.369629
| -0.641195
| -0.136
| -0.323
| -0.313
| null |
1
| 77,961
|
G
|
A
| false
|
Enhancer
| 2.628906
| -0.10487
| 1.236
| 0.614
| -0.077
| null |
1
| 79,772
|
C
|
G
| false
|
Enhancer
| -0.030762
| -0.138785
| -0.178
| -0.323
| -0.011
| null |
1
| 80,323
|
G
|
C
| false
|
Enhancer
| 0.372559
| -0.451047
| -0.196
| 0.663
| -0.183
| null |
1
| 80,619
|
G
|
A
| false
|
Enhancer
| 0.577148
| -0.207171
| -0.196
| -0.294
| -0.015
| null |
1
| 80,857
|
C
|
T
| false
|
Enhancer
| 1.063477
| -0.339268
| -0.147
| -0.268
| -0.004
| null |
1
| 81,260
|
C
|
T
| false
|
Enhancer
| -0.041992
| 0.073795
| 1.311
| 0.296
| -0.002
| null |
1
| 81,343
|
A
|
G
| false
|
Enhancer
| -2.310547
| -0.233605
| -0.165
| 0.415
| -0.051
| null |
1
| 82,163
|
G
|
A
| false
|
Enhancer
| 2.882813
| -0.124033
| -0.173
| -0.531
| -0.062
| null |
1
| 82,400
|
G
|
A
| false
|
Enhancer
| 2.724609
| -0.125267
| -0.173
| -0.293
| -0.026
| null |
1
| 82,562
|
T
|
C
| false
|
Enhancer
| 0.079102
| -0.234119
| -0.148
| -0.231
| -0.023
| null |
1
| 82,609
|
C
|
G
| false
|
Enhancer
| 0.246094
| -0.044349
| -0.147
| -0.295
| -0.013
| null |
1
| 82,676
|
T
|
G
| false
|
Enhancer
| -0.427246
| -0.580291
| -0.148
| -0.237
| -0.33
| null |
1
| 82,734
|
T
|
C
| false
|
Enhancer
| 0.005859
| -0.228981
| 1.694
| 0.658
| -0.031
| null |
1
| 83,084
|
T
|
A
| false
|
Enhancer
| 0.756836
| -0.016189
| 1.858
| 2.321
| -0.027
| null |
1
| 83,443
|
C
|
T
| false
|
Enhancer
| -0.074219
| -0.79636
| -0.147
| -0.087
| -0.352
| null |
1
| 83,795
|
G
|
A
| false
|
Enhancer
| -0.011719
| -0.052672
| 1.713
| 1.999
| -0.004
| null |
1
| 84,002
|
G
|
A
| false
|
Enhancer
| 0.780273
| -0.016299
| -0
| -0
| -0.022
| null |
1
| 84,244
|
A
|
C
| false
|
Enhancer
| -0.757324
| -0.049621
| -0.117
| -0.052
| -0.312
| null |
1
| 84,307
|
C
|
A
| false
|
Enhancer
| 0.730957
| 0.075284
| 2.015
| 2.345
| -0.046
| null |
1
| 84,683
|
A
|
G
| false
|
Enhancer
| -0.541992
| -0.230736
| 1.755
| 2.119
| -0.029
| null |
1
| 85,529
|
G
|
A
| false
|
Enhancer
| 2.621094
| -0.232815
| 1.711
| 0.801
| -0.175
| null |
1
| 85,597
|
A
|
C
| false
|
Enhancer
| -1.033203
| -0.552093
| -0.127
| -0.25
| -0.34
| null |
1
| 86,018
|
C
|
G
| false
|
Enhancer
| 0.283203
| -0.01549
| 2.28
| 2.175
| -0.061
| null |
1
| 86,065
|
G
|
C
| false
|
Enhancer
| -0.060547
| 0.014888
| -0.286
| -0.017
| -0.018
| null |
1
| 86,303
|
G
|
T
| false
|
Enhancer
| 0.916992
| 0.114918
| 0.851
| 0.493
| -0.012
| null |
1
| 86,331
|
A
|
G
| false
|
Enhancer
| -0.48877
| -0.167432
| -0.272
| -0.731
| -0.044
| null |
1
| 87,190
|
G
|
A
| false
|
Enhancer
| -1.007813
| -0.048625
| 1.499
| 2.304
| -0.005
| null |
1
| 88,136
|
G
|
A
| false
|
Enhancer
| -1.449219
| -0.215278
| -0.438
| -0.317
| -0.005
| null |
1
| 88,169
|
C
|
T
| false
|
Enhancer
| -2.121094
| -0.194336
| -0.371
| 0.702
| -0.038
| null |
1
| 88,172
|
G
|
A
| false
|
Enhancer
| 1.052734
| -0.170995
| -0.438
| 1.578
| -0.027
| null |
1
| 88,177
|
G
|
C
| false
|
Enhancer
| -3.109375
| -0.146098
| -0.438
| -0.322
| -0.023
| null |
1
| 89,599
|
A
|
T
| false
|
ncRNA
| -0.11084
| -0.198045
| -0.117
| 0.019
| -0.566
| 1.741074
|
1
| 89,946
|
A
|
T
| false
|
ncRNA
| -0.108887
| -0.170372
| -0.117
| 0.855
| -0.035
| -2.520203
|
1
| 90,007
|
G
|
A
| false
|
ncRNA
| -1.070313
| -0.155082
| -0.123
| -0.491
| -0.197
| -3.06636
|
1
| 91,190
|
G
|
A
| false
|
ncRNA
| 1.584961
| -0.247392
| -0.123
| 1.199
| -0.065
| -0.367081
|
1
| 91,421
|
T
|
C
| false
|
ncRNA
| -1.962891
| -0.506171
| 1.639
| 2.426
| -0.261
| -1.994446
|
1
| 91,605
|
C
|
T
| false
|
ncRNA
| 0.30127
| -0.311057
| -0.105
| -0.865
| -0.044
| 0.039276
|
1
| 131,310
|
G
|
C
| false
|
ncRNA
| -2.480469
| -0.227829
| -0.679
| -6.959
| -0.002
| -0.085175
|
1
| 133,160
|
G
|
A
| false
|
ncRNA
| -0.618164
| -0.173938
| 0.488
| -1.779
| -0
| -0.972931
|
1
| 133,483
|
G
|
T
| false
|
ncRNA
| -1.40918
| -0.139635
| -1.097
| 3.213
| -0.005
| 2.053314
|
1
| 136,437
|
T
|
C
| false
|
Promoter
| -0.912598
| -0.454278
| 2.884
| -0
| -0
| 4.047104
|
1
| 136,635
|
T
|
G
| false
|
Promoter
| 1.493164
| -0.687213
| 0.24
| -0
| -0
| -5.361816
|
1
| 136,817
|
T
|
C
| false
|
Promoter
| 0.622559
| -0.775266
| 2.258
| -0
| -0
| -6.990189
|
1
| 137,825
|
G
|
A
| false
|
ncRNA
| 0.962402
| -0.320727
| 0.026
| null | -0.001
| -1.20256
|
1
| 138,593
|
G
|
T
| false
|
Promoter
| -1.613281
| -0.08484
| -0.436
| null | -0.008
| -3.858597
|
1
| 181,321
|
C
|
G
| false
|
Enhancer
| 0.117188
| -0.501456
| null | -0.076
| null | null |
1
| 181,583
|
C
|
G
| false
|
Enhancer
| -0.749023
| -0.469966
| null | -0.092
| null | null |
1
| 181,706
|
G
|
A
| false
|
Promoter
| -0.556152
| -0.434034
| null | -0.091
| null | -1.906433
|
1
| 183,800
|
C
|
G
| false
|
ncRNA
| -5.15625
| -0.875078
| -6.08
| -4.848
| -0.949
| 0.199371
|
1
| 185,497
|
G
|
A
| false
|
ncRNA
| -3.074219
| -1.825089
| -1.285
| -4.388
| -0.995
| -0.233536
|
1
| 187,153
|
T
|
C
| false
|
ncRNA
| -2.976563
| -0.430129
| -0.258
| 1.506
| -0.018
| -1.609665
|
1
| 187,259
|
G
|
T
| false
|
ncRNA
| 1.665039
| 0.607216
| 5.309
| 20
| -0
| 1.677856
|
1
| 188,252
|
G
|
T
| false
|
ncRNA
| -4.585938
| -0.983406
| -1.126
| -2.935
| -1
| -1.500809
|
1
| 202,330
|
C
|
A
| false
|
Enhancer
| -1.375
| -0.763342
| 0.171
| -0.868
| -0
| null |
1
| 206,074
|
T
|
C
| false
|
Enhancer
| 1.161133
| -0.530138
| 0.168
| 0.374
| -0
| null |
1
| 206,849
|
C
|
G
| false
|
Enhancer
| -2.746094
| -0.431993
| -0.038
| -0.435
| -0.001
| null |
1
| 206,863
|
T
|
C
| false
|
Enhancer
| 3.609375
| -1.287873
| -0.84
| -2.68
| -0.646
| null |
1
| 206,930
|
G
|
A
| false
|
Enhancer
| 3.951172
| -1.07014
| -0.231
| -0.577
| -0.991
| null |
1
| 263,722
|
C
|
G
| false
|
ncRNA
| 0.079102
| 0.263589
| 2.308
| -0.586
| -0
| -2.308746
|
1
| 264,481
|
G
|
A
| false
|
ncRNA
| 1.994141
| -0.15525
| 1.718
| 1.218
| -0.001
| 3.506775
|
1
| 264,557
|
A
|
G
| false
|
ncRNA
| 0.164063
| -0.399896
| 0.643
| 0.181
| -0
| 0.392944
|
1
| 264,562
|
C
|
T
| false
|
ncRNA
| 0.09375
| -0.150344
| 0.781
| 0.249
| -0.001
| 0.075928
|
End of preview. Expand
in Data Studio
OMIM variants
For more information check out our paper and repository.
Usage
- Pandas
import pandas as pd
df = pd.read_parquet("hf://datasets/songlab/omim/test.parquet")
- Polars
import polars as pl
df = pl.read_parquet("https://huggingface.co/datasets/songlab/omim/resolve/main/test.parquet")
- Datasets
from datasets import load_dataset
dataset = load_dataset("songlab/omim", split="test")
- Downloads last month
- 76
Size of downloaded dataset files:
45 MB
Size of the auto-converted Parquet files:
45 MB
Number of rows:
2,640,672