GPN-MSA
Collection
https://www.biorxiv.org/content/10.1101/2023.10.10.561776v1
•
8 items
•
Updated
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 |
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gnomAD variants
For more information check out our paper and repository.
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")
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