GPN-MSA
Collection
https://www.nature.com/articles/s41587-024-02511-w
•
11 items
•
Updated
•
5
Dataset Viewer
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chrom
large_stringlengths 1
2
| pos
int64 10.1k
249M
| ref
large_stringlengths 1
1
| alt
large_stringlengths 1
1
| label
bool 2
classes | consequence
large_stringlengths 6
26
| GPN-MSA
float32 -13.98
12.6
⌀ | CADD
float32 -21.01
18.7
| phyloP-100v
float64 -10
20
⌀ | phyloP-241m
float64 -9.28
20
⌀ | phastCons-100v
float64 -1
-0
⌀ | ESM-1b
float64 -25.92
12
⌀ | SpliceAI
float32 -1
-0
⌀ |
|---|---|---|---|---|---|---|---|---|---|---|---|---|
1
| 10,111
|
C
|
A
| true
|
intergenic
| -0.017578
| -0.550283
| null | -0
| null | null | null |
1
| 10,131
|
C
|
A
| true
|
intergenic
| -0.347656
| -0.549423
| null | -0
| null | null | null |
1
| 10,139
|
A
|
T
| true
|
intergenic
| -0.432617
| -0.687144
| null | -0
| null | null | null |
1
| 10,141
|
C
|
G
| true
|
intergenic
| -0.496094
| -0.565436
| null | -0
| null | null | null |
1
| 10,154
|
C
|
A
| true
|
intergenic
| -0.009766
| -0.546682
| null | -0
| null | null | null |
1
| 10,172
|
C
|
G
| true
|
intergenic
| -0.439453
| -0.56446
| null | -0
| null | null | null |
1
| 10,193
|
A
|
T
| true
|
intergenic
| -0.429688
| -0.6845
| null | -0
| null | null | null |
1
| 10,202
|
C
|
G
| true
|
intergenic
| -2.82666
| -0.556766
| null | -0
| null | null | null |
1
| 10,210
|
T
|
G
| true
|
intergenic
| -1.92981
| -0.697907
| null | -0
| null | null | null |
1
| 10,218
|
A
|
G
| true
|
intergenic
| -0.486328
| -0.710005
| null | -0
| null | null | null |
1
| 10,227
|
C
|
T
| true
|
intergenic
| -0.634766
| -0.590154
| null | -0
| null | null | null |
1
| 10,371
|
A
|
C
| true
|
intergenic
| 0.082031
| -0.676272
| null | -0
| null | null | null |
1
| 10,376
|
A
|
C
| true
|
intergenic
| 0.382813
| -0.676288
| null | -0
| null | null | null |
1
| 10,408
|
A
|
G
| true
|
intergenic
| -0.31543
| -0.676011
| null | -0
| null | null | null |
1
| 10,411
|
C
|
G
| true
|
intergenic
| -2.672607
| -0.523908
| null | -0
| null | null | null |
1
| 10,427
|
A
|
G
| true
|
intergenic
| -0.367188
| -0.723995
| null | 1.853
| null | null | null |
1
| 10,430
|
C
|
T
| true
|
intergenic
| -0.791992
| -0.602602
| null | 1.907
| null | null | null |
1
| 10,435
|
C
|
G
| true
|
intergenic
| -1.984863
| -0.561203
| null | 1.823
| null | null | null |
1
| 10,447
|
C
|
T
| true
|
intergenic
| -0.475586
| -0.604101
| null | 1.823
| null | null | null |
1
| 10,453
|
C
|
G
| true
|
intergenic
| -0.354492
| -0.572278
| null | 1.823
| null | null | null |
1
| 10,466
|
C
|
T
| true
|
intergenic
| -0.552734
| -0.610463
| null | -0.092
| null | null | null |
1
| 10,478
|
C
|
G
| true
|
intergenic
| -1.476563
| -0.614099
| null | -0.092
| null | null | null |
1
| 10,491
|
C
|
G
| true
|
intergenic
| -0.095703
| -0.621122
| null | -0.092
| null | null | null |
1
| 10,506
|
C
|
G
| true
|
intergenic
| 0.262695
| -0.555395
| null | -0.092
| null | null | null |
1
| 10,514
|
G
|
C
| true
|
intergenic
| -0.224609
| -0.543728
| null | 1.821
| null | null | null |
1
| 10,519
|
G
|
A
| true
|
intergenic
| -1.178223
| -0.590625
| null | 1.815
| null | null | null |
1
| 10,550
|
G
|
A
| true
|
intergenic
| -0.987305
| -0.672059
| null | -0.091
| null | null | null |
1
| 10,558
|
G
|
C
| true
|
intergenic
| 0.006836
| -0.645361
| null | -0.091
| null | null | null |
1
| 10,565
|
C
|
T
| true
|
intergenic
| -1.271484
| -0.724869
| null | -0.092
| null | null | null |
1
| 10,571
|
C
|
T
| true
|
intergenic
| 0.186523
| -0.735859
| null | -0.092
| null | null | null |
1
| 10,581
|
G
|
A
| true
|
intergenic
| -0.921875
| -0.705439
| null | 1.73
| null | null | null |
1
| 10,584
|
C
|
A
| true
|
intergenic
| -0.963379
| -0.678982
| null | -0.092
| null | null | null |
1
| 10,596
|
G
|
C
| true
|
intergenic
| 0.310547
| -0.730547
| null | -0.091
| null | null | null |
1
| 10,598
|
G
|
A
| true
|
intergenic
| -1.321289
| -0.767249
| null | -0.091
| null | null | null |
1
| 10,601
|
G
|
A
| true
|
intergenic
| -1.342773
| -0.475697
| null | -0.091
| null | null | null |
1
| 10,690
|
G
|
C
| true
|
intergenic
| -0.446289
| -0.592865
| null | -0.075
| null | null | null |
1
| 10,765
|
G
|
A
| true
|
intergenic
| -1.17334
| -0.598721
| null | -0.075
| null | null | null |
1
| 10,796
|
G
|
A
| true
|
intergenic
| -1.084473
| -0.644714
| null | -0.075
| null | null | null |
1
| 10,825
|
G
|
A
| true
|
intergenic
| -1.117188
| -0.587941
| null | -0.075
| null | null | null |
1
| 10,835
|
A
|
C
| true
|
intergenic
| 0.37793
| -0.700726
| null | -0.062
| null | null | null |
1
| 10,837
|
G
|
C
| true
|
intergenic
| -0.166016
| -0.528688
| null | -0.075
| null | null | null |
1
| 10,888
|
G
|
T
| true
|
upstream_gene
| -0.37793
| -0.506465
| null | -0.091
| null | null | null |
1
| 10,918
|
G
|
C
| true
|
upstream_gene
| -0.478516
| -0.508929
| -0.064
| 1.719
| -0.253
| null | null |
1
| 10,926
|
C
|
A
| true
|
upstream_gene
| -0.97168
| -0.505901
| -0.055
| -0.092
| -0.234
| null | null |
1
| 10,932
|
G
|
A
| true
|
upstream_gene
| -0.756836
| -0.511043
| -0.064
| -0.091
| -0.213
| null | null |
1
| 12,998
|
C
|
G
| true
|
non_coding_transcript_exon
| -6.367188
| -1.086314
| -5.829
| -2.392
| -0.987
| null | null |
1
| 13,007
|
G
|
C
| true
|
non_coding_transcript_exon
| -4.580811
| -1.016434
| -2.321
| -4.924
| -0.998
| null | null |
1
| 13,014
|
T
|
C
| true
|
non_coding_transcript_exon
| -4.552734
| -1.392085
| -3.488
| -2.898
| -1
| null | null |
1
| 13,023
|
T
|
C
| true
|
non_coding_transcript_exon
| -4.335938
| -1.130192
| -3.394
| -6.335
| -1
| null | null |
1
| 13,073
|
C
|
A
| true
|
intron
| -1.723633
| 0.000539
| 0.6
| 0.357
| -0
| null | null |
1
| 13,076
|
G
|
A
| true
|
intron
| -0.282227
| 0.235741
| 0.749
| 0.146
| -0
| null | null |
1
| 13,101
|
G
|
C
| true
|
intron
| -1.663574
| -0.495559
| -0.303
| -1.553
| -0
| null | null |
1
| 13,105
|
G
|
C
| true
|
intron
| -0.314453
| 0.268652
| 0.468
| 1.041
| -0
| null | null |
1
| 13,143
|
G
|
C
| true
|
intron
| -1.569824
| -0.209009
| 0.649
| -0.126
| -0
| null | null |
1
| 13,156
|
G
|
C
| true
|
intron
| -0.786133
| 0.370603
| 0.898
| -0.121
| -0
| null | null |
1
| 13,158
|
G
|
T
| true
|
intron
| -1.439941
| 0.206569
| 0.146
| 1.293
| -0
| null | null |
1
| 13,193
|
C
|
G
| true
|
intron
| -1.280273
| 0.732305
| 2.422
| 1.896
| -0
| null | null |
1
| 13,230
|
T
|
G
| true
|
non_coding_transcript_exon
| -6.16748
| -1.132359
| -4.18
| -2.942
| -1
| null | null |
1
| 13,233
|
G
|
C
| true
|
non_coding_transcript_exon
| -6.283203
| -1.125951
| -7.222
| -6.997
| -1
| null | null |
1
| 13,257
|
T
|
C
| true
|
non_coding_transcript_exon
| -3.228516
| -1.089472
| -4.339
| -3.714
| -1
| null | null |
1
| 13,267
|
G
|
C
| true
|
non_coding_transcript_exon
| -5.69873
| -0.911416
| -1.237
| -4.122
| -1
| null | null |
1
| 13,268
|
G
|
C
| true
|
non_coding_transcript_exon
| -4.865234
| -1.164731
| -7.346
| -6.946
| -1
| null | null |
1
| 13,273
|
G
|
C
| false
|
non_coding_transcript_exon
| -4.07251
| -0.398596
| -1.091
| -0.864
| -1
| null | null |
1
| 13,290
|
C
|
T
| true
|
non_coding_transcript_exon
| -3.74707
| -0.470147
| -1.35
| -1.66
| -0.003
| null | null |
1
| 13,304
|
C
|
A
| true
|
non_coding_transcript_exon
| -4.040771
| -0.477425
| -0.924
| -3.005
| -0.999
| null | null |
1
| 13,306
|
G
|
A
| true
|
non_coding_transcript_exon
| -2.820313
| -0.363958
| -0.141
| -4.106
| -0.996
| null | null |
1
| 13,309
|
G
|
A
| true
|
non_coding_transcript_exon
| -1.852539
| 0.490557
| 2.131
| 8.585
| -0.001
| null | null |
1
| 13,326
|
T
|
G
| true
|
non_coding_transcript_exon
| 1.005859
| -0.354565
| -1.378
| -0.426
| -0.053
| null | null |
1
| 13,329
|
T
|
G
| true
|
non_coding_transcript_exon
| -4.488281
| -0.775557
| -1.787
| -4.615
| -0.3
| null | null |
1
| 13,335
|
T
|
A
| true
|
non_coding_transcript_exon
| -5.789063
| -0.823359
| -2.386
| -2.95
| -0.998
| null | null |
1
| 13,340
|
G
|
C
| true
|
non_coding_transcript_exon
| -4.693359
| -0.498724
| -0.233
| -2.028
| -0.005
| null | null |
1
| 13,358
|
A
|
G
| true
|
non_coding_transcript_exon
| -1.852295
| -0.244852
| -1.076
| -0.269
| -0.982
| null | null |
1
| 13,367
|
G
|
C
| true
|
non_coding_transcript_exon
| -0.089844
| 0.510896
| 1.513
| 6.727
| -0
| null | null |
1
| 13,382
|
C
|
A
| true
|
splice_region
| -4.155762
| -0.422578
| -0.391
| 0.094
| -0
| null | null |
1
| 13,461
|
G
|
C
| true
|
non_coding_transcript_exon
| -4.515289
| -0.942169
| -1.409
| -2.216
| -0.253
| null | null |
1
| 13,472
|
C
|
T
| true
|
non_coding_transcript_exon
| -2.685547
| -0.434868
| 0.036
| 0.716
| -0.017
| null | null |
1
| 13,480
|
C
|
G
| true
|
non_coding_transcript_exon
| -3.00293
| 0.394461
| 1.002
| 2.569
| -0.003
| null | null |
1
| 13,487
|
C
|
A
| true
|
non_coding_transcript_exon
| -1.461914
| -0.148622
| 0.65
| 0.28
| -0
| null | null |
1
| 13,489
|
G
|
A
| true
|
non_coding_transcript_exon
| -1.233398
| -0.044051
| 0.637
| 2.299
| -0
| null | null |
1
| 13,584
|
A
|
G
| true
|
non_coding_transcript_exon
| -1.28418
| -0.104195
| 0.539
| -0.396
| -0
| null | null |
1
| 13,610
|
G
|
C
| true
|
non_coding_transcript_exon
| -1.047852
| -0.035386
| 0.272
| 0.218
| -0
| null | null |
1
| 13,712
|
A
|
T
| true
|
non_coding_transcript_exon
| -1.293945
| -0.192838
| 0.37
| 0.367
| -0
| null | null |
1
| 13,851
|
C
|
T
| true
|
non_coding_transcript_exon
| -0.591797
| -0.003397
| 1.173
| -0.087
| -0
| null | null |
1
| 13,918
|
C
|
A
| true
|
non_coding_transcript_exon
| -1.486328
| -0.394646
| -0.392
| -0.861
| -0.004
| null | null |
1
| 13,934
|
C
|
T
| true
|
non_coding_transcript_exon
| -1.389648
| -0.328415
| 0.064
| -0.175
| -0
| null | null |
1
| 13,951
|
G
|
C
| true
|
non_coding_transcript_exon
| -1.200195
| 0.199525
| 0.758
| -0.547
| -0
| null | null |
1
| 14,065
|
T
|
C
| true
|
non_coding_transcript_exon
| -2.557617
| -0.845538
| 0.225
| 0.652
| -0
| null | null |
1
| 14,092
|
G
|
C
| true
|
non_coding_transcript_exon
| -3.862305
| -0.631029
| -1.715
| -3.189
| -0.096
| null | null |
1
| 14,152
|
T
|
A
| true
|
non_coding_transcript_exon
| -5.156006
| -1.418721
| -0.375
| -0.4
| -0.989
| null | null |
1
| 14,184
|
C
|
T
| true
|
non_coding_transcript_exon
| -5.110352
| -1.558891
| -2.634
| -5.043
| -0.835
| null | null |
1
| 14,185
|
T
|
A
| true
|
non_coding_transcript_exon
| -5.406738
| -1.248153
| -0.334
| -1.427
| -0.394
| null | null |
1
| 14,192
|
G
|
A
| true
|
non_coding_transcript_exon
| -2.666992
| -0.803716
| -0.623
| -1.235
| -0.017
| null | null |
1
| 14,196
|
C
|
A
| true
|
non_coding_transcript_exon
| -2.134766
| -0.324873
| 0.727
| -1.424
| -0.001
| null | null |
1
| 14,283
|
G
|
A
| true
|
non_coding_transcript_exon
| -1.863281
| -0.444287
| -0.691
| -0.062
| -0.054
| null | null |
1
| 14,302
|
C
|
T
| true
|
non_coding_transcript_exon
| -0.374023
| -0.247199
| 0.418
| 1.011
| -0
| null | null |
1
| 14,374
|
A
|
G
| true
|
non_coding_transcript_exon
| -1.019531
| -0.198752
| 0.377
| 5.365
| -0
| null | null |
1
| 14,390
|
A
|
G
| true
|
non_coding_transcript_exon
| -2.491211
| -0.688573
| -1.048
| -0.753
| -0.011
| null | null |
1
| 14,392
|
G
|
T
| true
|
non_coding_transcript_exon
| -2.540283
| -0.34352
| -0.085
| -1.459
| -0.001
| null | null |
1
| 14,422
|
T
|
A
| true
|
non_coding_transcript_exon
| -5.578125
| -0.831683
| -0.641
| -0.158
| -0.184
| null | null |
1
| 14,428
|
G
|
C
| true
|
non_coding_transcript_exon
| 3.122498
| 0.134148
| 0.544
| -0.402
| -0
| null | null |
End of preview. Expand
in Data Studio
gnomAD variants
For more information check out our paper and repository.
Labels
| Label | Meaning |
|---|---|
| True | Rare, singleton (AC=1) |
| False | Common (MAF > 5%) |
Note that the label does not indicate deleteriousness/pathogenicity. This is not suitable for a classification task. We recommend calculating enrichment or rare variants at the tail of model scores.
Usage
- Pandas
import pandas as pd
df = pd.read_parquet("hf://datasets/songlab/gnomad/test.parquet")
- Polars
import polars as pl
df = pl.read_parquet("https://huggingface.co/datasets/songlab/gnomad/resolve/main/test.parquet")
- Datasets
from datasets import load_dataset
dataset = load_dataset("songlab/gnomad", split="test")
- Downloads last month
- 17
Size of downloaded dataset files:
4.2 GB
Size of the auto-converted Parquet files:
4.2 GB
Number of rows:
262,586,201