GPN-MSA
Collection
https://www.biorxiv.org/content/10.1101/2023.10.10.561776v1
•
9 items
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Updated
Datasets:
chrom
large_stringlengths 1
2
| pos
int64 14.9k
249M
| ref
large_stringlengths 1
1
| alt
large_stringlengths 1
1
| label
bool 2
classes | GPN-MSA
float32 -13.66
12.6
| CADD
float64 -12.41
4.33
| phyloP-100v
float64 -10
20
⌀ | phyloP-241m
float64 -8.9
20
⌀ | phastCons-100v
float64 -1
-0
⌀ | ESM-1b
float64 -25.89
12
⌀ | NT
float32 -11.48
9.93
⌀ | HyenaDNA
float32 -0
0
|
|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 | 69,511 | A | G | false | 1.493164 | -0.112916 | 0.684 | -3.29 | -0 | null | -1.597534 | -0.000001 |
1 | 953,279 | T | C | false | 2.578125 | -0.266107 | -0.037 | -1.27 | -0.009 | -2.88 | -0.583755 | -0.000001 |
1 | 973,858 | G | C | false | 1.5625 | -0.787153 | 0.431 | -0.835 | -0 | -2.538 | 1.60527 | -0.000001 |
1 | 973,929 | T | C | false | -1.328125 | -0.818047 | -0.076 | 0.539 | -0.001 | -3.377 | 0.537186 | -0.000001 |
1 | 978,953 | C | G | false | 1.72168 | 0.096301 | 0.22 | 0.223 | -0 | -3.781 | 0.034943 | -0.000002 |
1 | 999,842 | C | A | false | -1.387695 | -0.472275 | 0.582 | 1.508 | -0 | null | -1.683807 | -0.000004 |
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1 | 1,050,575 | G | C | true | -10.625 | -4.095325 | -9.276 | -8.514 | -1 | -13.196 | -2.032928 | -0.000002 |
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1 | 1,179,288 | G | A | false | 0.321289 | -0.167083 | 0.447 | -0.13 | -0 | -3.748 | 0.075058 | 0 |
1 | 1,180,851 | T | C | false | 1.851563 | -0.21429 | -0.026 | -1.845 | -0 | -2.236 | 1.076035 | 0.000001 |
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1 | 1,211,863 | A | C | false | -1.439453 | -0.136844 | 0.141 | -0.007 | -0.002 | null | 1.88829 | 0.000002 |
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1 | 1,212,898 | C | T | false | -0.602051 | -0.438368 | 0.235 | 4.258 | -0 | null | 1.300079 | 0.000001 |
1 | 1,213,738 | G | A | true | -2.636719 | -1.622702 | 0.097 | -0.521 | -0 | -9.152 | 1.156631 | 0.000001 |
1 | 1,232,279 | A | G | true | -6.527344 | -2.298613 | -2.027 | -1.886 | -0.925 | null | -5.417542 | 0.000003 |
1 | 1,232,280 | T | C | true | -7.273438 | -2.745302 | -1.175 | -3.189 | -0.99 | null | -5.90274 | 0.000002 |
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1 | 1,232,744 | G | A | true | -9.640625 | -4.68026 | -7.4 | -5.604 | -1 | -10.741 | -2.074203 | -0.000002 |
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1 | 1,232,800 | G | C | false | -1.115234 | -0.830179 | -0.466 | 1.097 | -0.998 | -2.994 | 0.637238 | -0 |
1 | 1,232,834 | T | C | true | -7.078125 | -4.516843 | -3.777 | -3.569 | -1 | -6.756 | -1.654037 | 0.000001 |
1 | 1,232,896 | C | G | true | -7.371094 | -3.667146 | 0.325 | 0.168 | -0.335 | -14.467 | -1.367035 | 0.000001 |
1 | 1,232,897 | G | C | true | -9.765625 | -4.542989 | -6.691 | -8.625 | -1 | -10.692 | -0.255386 | 0.000001 |
1 | 1,232,927 | G | A | true | -8.359375 | -4.493109 | -6.663 | -8.626 | -1 | -13.48 | -1.325531 | 0 |
1 | 1,233,044 | C | T | true | -8.429688 | -4.400743 | -2.068 | -8.797 | -1 | -12.325 | 0.336212 | -0.000002 |
1 | 1,233,177 | G | C | true | -7.246094 | -4.25814 | -5.541 | -6.948 | -1 | -13.798 | 0.070724 | 0.000001 |
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1 | 1,285,621 | A | G | false | -1.320313 | -1.028294 | 1.673 | 0.04 | -0 | -2.734 | -1.318069 | -0.000001 |
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1 | 1,291,377 | G | A | false | 0.023026 | -0.44613 | 0.087 | -1.21 | -0 | -4.715 | 0.394531 | 0.000001 |
1 | 1,291,509 | G | A | false | 0.664063 | 0.265035 | 2.719 | 4.19 | -0 | -4.258 | 0.970993 | 0.000002 |
1 | 1,312,290 | C | T | true | -5.15625 | -3.357409 | -4.362 | -6.917 | -1 | -5.937 | 0.267563 | -0.000003 |
1 | 1,312,841 | G | A | true | -7.707031 | -3.542766 | -8.924 | -6.83 | -1 | -11.352 | -0.052994 | -0.000001 |
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1 | 1,320,493 | C | T | true | -7.183594 | -2.847095 | -7.635 | -8.743 | -1 | -8.887 | -0.051239 | 0.000002 |
1 | 1,321,072 | C | A | true | -13.140625 | -4.400157 | -7.661 | -8.745 | -1 | -16.121 | -1.335587 | 0.000002 |
1 | 1,332,271 | G | A | false | -0.956543 | 0.611933 | 2.457 | 4.275 | -0 | -3.367 | 0.004333 | -0.000001 |
1 | 1,334,108 | G | A | false | -0.147461 | -0.004351 | -0.198 | 1.406 | -0 | -6.573 | -0.596497 | 0 |
1 | 1,420,203 | C | A | false | -1.3125 | -2.239272 | 1.246 | -0.527 | -0 | -10.381 | -4.443069 | 0 |
1 | 1,426,261 | C | T | false | 1.09375 | -0.466194 | 0.724 | -0.952 | -0 | -1.575 | 0.268402 | -0.000002 |
1 | 1,452,384 | G | A | false | -4.957031 | -4.322648 | -8.17 | -8.528 | -1 | -13.144 | -2.093872 | -0.000001 |
1 | 1,495,605 | C | T | false | -1.003906 | -0.735766 | 0.688 | 0.039 | -0 | -4.705 | -0.573624 | 0.000004 |
1 | 1,512,312 | G | A | false | -5.585938 | -2.55411 | -3.349 | -8.396 | -0.999 | -3.698 | -1.577408 | -0.000001 |
1 | 1,516,036 | T | G | true | -8.304688 | -3.368562 | -6.341 | -6.275 | -0.992 | -3.651 | 0.092316 | -0.000003 |
1 | 1,517,186 | G | A | false | -1.466797 | -0.71163 | -1.385 | -2.202 | -0.011 | -4.841 | -2.204987 | -0.000002 |
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1 | 1,535,616 | G | A | true | -8.273438 | -4.118985 | -2.772 | -6.783 | -1 | -4.685 | -0.149643 | 0.000001 |
1 | 1,535,723 | G | A | true | -6.683594 | -3.741044 | -5.617 | -8.586 | -1 | -4.354 | -0.082504 | -0 |
1 | 1,616,547 | T | C | false | 1.503906 | -0.54761 | 0.394 | 0.175 | -0 | null | 1.108597 | 0.000002 |
1 | 1,640,423 | C | T | false | -4.613281 | -2.384015 | -5.637 | -3.468 | -0.995 | -7.286 | 0.570633 | -0 |
1 | 1,641,819 | C | T | false | 0.884766 | -0.617502 | -0.039 | 0.278 | -0.987 | null | 2.53569 | 0.000004 |
1 | 1,668,373 | C | T | false | -3.203125 | -1.409952 | -3.753 | -2.372 | -0.998 | -5.63 | 0.984894 | 0.000001 |
1 | 1,668,449 | A | G | false | 0.150391 | 0.356083 | 0.521 | 3.961 | -0.048 | null | 0.568039 | -0.000001 |
1 | 1,707,486 | C | T | false | -2.923828 | -1.558467 | -3.757 | -6.882 | -0.998 | -10.252 | -2.041031 | -0 |
1 | 1,707,555 | C | T | false | -3.8125 | -2.087687 | -4.923 | -3.468 | -0.984 | -7.325 | 0.57814 | -0 |
1 | 1,719,406 | G | A | false | -1.825195 | -4.246027 | -6.251 | -5.87 | -1 | -7.366 | -0.257889 | 0.000003 |
1 | 1,754,601 | G | T | false | -6.25 | 0.4479 | 1.13 | 6.418 | -0.005 | -5.367 | -1.039474 | -0.000002 |
1 | 1,804,496 | T | C | true | -11.46875 | -4.523403 | -7.839 | -6.134 | -1 | -15.496 | -2.27919 | 0.000002 |
1 | 1,804,497 | C | A | true | -12.976563 | -4.21045 | -7.729 | -8.579 | -1 | -15.91 | -4.677444 | -0 |
1 | 1,804,502 | C | A | true | -12.234375 | -3.918063 | -7.729 | -8.579 | -1 | -17.041 | -0.676041 | 0.000001 |
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1 | 1,804,562 | C | A | true | -12.109375 | -3.636235 | -7.729 | -8.579 | -1 | -16.534 | 0.598404 | 0.000004 |
1 | 1,806,503 | A | T | true | -13.328125 | -4.256918 | -9.083 | -5.836 | -1 | -13.221 | -0.786102 | 0.000001 |
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1 | 1,916,540 | T | C | false | 2.607422 | -1.204282 | 0.175 | 1.396 | -0 | 2.522 | 2.444244 | 0 |
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1 | 1,923,833 | C | G | true | -7.753906 | -3.512015 | -2.846 | -8.659 | -1 | -7.584 | 0.223419 | 0 |
1 | 1,927,024 | C | T | true | -1.996094 | -0.783969 | -0.382 | -0.03 | -0 | -5.316 | 0.951736 | 0.000002 |
1 | 1,927,692 | C | T | false | 0.583008 | 1.649318 | 3.588 | 5.924 | -0 | -4.229 | 1.1642 | -0 |
1 | 1,927,737 | T | C | false | 1.25293 | -0.435867 | 0.144 | -3.951 | -0 | -2.232 | 0.508667 | 0 |
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1 | 1,942,086 | T | C | false | 3.904297 | -1.532497 | -2.516 | -1.494 | -0.999 | -7.38 | -0.642532 | 0 |
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1 | 1,968,793 | T | C | false | 2.328125 | 0.478732 | -0.054 | -0.904 | -0.001 | -4.6 | -1.323013 | -0 |
1 | 1,970,722 | C | T | true | -6.839844 | -3.017338 | -3.879 | -8.484 | -0.98 | 0.197 | 1.7453 | -0 |
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1 | 2,025,598 | T | C | false | 3.611328 | -1.082832 | 1.217 | -0.193 | -0 | null | 3.628601 | 0.000001 |
1 | 2,029,197 | C | G | true | -9.546875 | -3.146233 | -2.655 | -5.777 | -1 | -9.72 | -0.509109 | -0.000006 |
1 | 2,029,235 | C | T | false | -0.580078 | -0.219853 | 0.476 | 1.463 | -0.112 | null | -2.706818 | -0.000001 |
1 | 2,193,733 | G | A | false | -1.341797 | -0.285874 | 0.118 | -0.297 | -0 | -4.024 | -1.122803 | -0.000001 |
1 | 2,228,825 | C | T | true | -7.746094 | -3.865474 | -6.406 | -5.785 | -1 | -6.082 | 0.461075 | -0.000002 |
1 | 2,228,828 | T | G | true | -10.546875 | -3.488515 | -4.895 | -3.829 | -1 | -13.829 | -1.652863 | 0.000001 |
1 | 2,228,848 | T | A | true | -7.722656 | -2.8778 | -1.305 | -3.824 | -1 | -5.263 | 0.304794 | 0 |
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ClinVar variants
For more information check out our paper and repository.
Usage
- Pandas
import pandas as pd
df = pd.read_parquet("hf://datasets/songlab/clinvar/test.parquet")
- Polars
import polars as pl
df = pl.read_parquet("https://huggingface.co/datasets/songlab/clinvar/resolve/main/test.parquet")
- Datasets
from datasets import load_dataset
dataset = load_dataset("songlab/clinvar", split="test")
- Downloads last month
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Size of downloaded dataset files:
1.15 MB
Size of the auto-converted Parquet files:
1.15 MB
Number of rows:
40,976