chrom
stringclasses 24
values | pos
int64 10.2k
249M
| ref
stringclasses 4
values | alt
stringclasses 4
values | label
stringclasses 4
values | source
stringclasses 4
values | consequence
stringlengths 9
465
| id
stringlengths 1
7
⌀ | review_status
stringclasses 5
values | GENOMIC_MUTATION_ID
stringlengths 12
12
⌀ | n_samples
float64 44
1.46k
⌀ | total_samples
float64 43.2k
43.2k
⌀ | freq
float64 0
0.03
⌀ | OMIM
stringlengths 3
10
⌀ | Gene
stringlengths 2
8
⌀ | PMID
float64 1.37M
26.6M
⌀ | AC
float64 1
152k
⌀ | AN
float64 140k
152k
⌀ | AF
float64 0
1
⌀ | MAF
float64 0
0.5
⌀ | MAC
float64 1
76.1k
⌀ |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 | 14,731 | G | A | Rare | gnomAD | downstream_gene_variant,intron_variant&non_coding_transcript_variant,non_coding_transcript_exon_variant | null | null | null | null | null | null | null | null | null | 1 | 148,066 | 0.000007 | 0.000007 | 1 |
1 | 16,487 | T | C | Common | gnomAD | downstream_gene_variant,intron_variant&non_coding_transcript_variant,regulatory_region_variant | null | null | null | null | null | null | null | null | null | 9,468 | 140,496 | 0.06739 | 0.06739 | 9,468 |
1 | 62,015 | C | G | Rare | gnomAD | intron_variant&non_coding_transcript_variant,upstream_gene_variant | null | null | null | null | null | null | null | null | null | 1 | 141,416 | 0.000007 | 0.000007 | 1 |
1 | 62,046 | A | T | Rare | gnomAD | intron_variant&non_coding_transcript_variant,upstream_gene_variant | null | null | null | null | null | null | null | null | null | 1 | 140,080 | 0.000007 | 0.000007 | 1 |
1 | 64,866 | T | G | Rare | gnomAD | downstream_gene_variant,upstream_gene_variant | null | null | null | null | null | null | null | null | null | 1 | 140,214 | 0.000007 | 0.000007 | 1 |
1 | 103,238 | G | A | Rare | gnomAD | intron_variant&non_coding_transcript_variant | null | null | null | null | null | null | null | null | null | 1 | 150,128 | 0.000007 | 0.000007 | 1 |
1 | 105,345 | A | C | Rare | gnomAD | intron_variant&non_coding_transcript_variant,regulatory_region_variant | null | null | null | null | null | null | null | null | null | 1 | 141,080 | 0.000007 | 0.000007 | 1 |
1 | 109,400 | T | C | Rare | gnomAD | downstream_gene_variant,intron_variant&non_coding_transcript_variant | null | null | null | null | null | null | null | null | null | 1 | 151,200 | 0.000007 | 0.000007 | 1 |
1 | 113,810 | C | A | Rare | gnomAD | intron_variant&non_coding_transcript_variant | null | null | null | null | null | null | null | null | null | 1 | 149,284 | 0.000007 | 0.000007 | 1 |
1 | 123,901 | C | G | Rare | gnomAD | intron_variant&non_coding_transcript_variant,upstream_gene_variant | null | null | null | null | null | null | null | null | null | 1 | 150,578 | 0.000007 | 0.000007 | 1 |
1 | 124,013 | A | C | Rare | gnomAD | intron_variant&non_coding_transcript_variant,upstream_gene_variant | null | null | null | null | null | null | null | null | null | 1 | 151,388 | 0.000007 | 0.000007 | 1 |
1 | 126,113 | C | A | Common | gnomAD | downstream_gene_variant,intron_variant&non_coding_transcript_variant,upstream_gene_variant | null | null | null | null | null | null | null | null | null | 135,835 | 144,502 | 0.940022 | 0.059978 | 8,667 |
1 | 126,359 | A | G | Rare | gnomAD | downstream_gene_variant,intron_variant&non_coding_transcript_variant,upstream_gene_variant | null | null | null | null | null | null | null | null | null | 1 | 151,760 | 0.000007 | 0.000007 | 1 |
1 | 129,315 | A | G | Common | gnomAD | intron_variant&non_coding_transcript_variant,upstream_gene_variant | null | null | null | null | null | null | null | null | null | 15,364 | 144,124 | 0.106603 | 0.106603 | 15,364 |
1 | 133,160 | G | A | Common | gnomAD | downstream_gene_variant,intron_variant&non_coding_transcript_variant,non_coding_transcript_exon_variant,upstream_gene_variant | null | null | null | null | null | null | null | null | null | 13,758 | 148,950 | 0.092367 | 0.092367 | 13,758 |
1 | 133,194 | C | G | Rare | gnomAD | downstream_gene_variant,intron_variant&non_coding_transcript_variant,non_coding_transcript_exon_variant,upstream_gene_variant | null | null | null | null | null | null | null | null | null | 1 | 151,700 | 0.000007 | 0.000007 | 1 |
1 | 133,483 | G | T | Common | gnomAD | downstream_gene_variant,intron_variant&non_coding_transcript_variant,non_coding_transcript_exon_variant,upstream_gene_variant | null | null | null | null | null | null | null | null | null | 44,261 | 143,434 | 0.308581 | 0.308581 | 44,261 |
1 | 135,040 | T | C | Common | gnomAD | downstream_gene_variant,intron_variant&non_coding_transcript_variant,non_coding_transcript_exon_variant,regulatory_region_variant,upstream_gene_variant | null | null | null | null | null | null | null | null | null | 13,459 | 148,318 | 0.090744 | 0.090744 | 13,459 |
1 | 137,825 | G | A | Common | gnomAD | downstream_gene_variant,intron_variant&non_coding_transcript_variant,non_coding_transcript_exon_variant,regulatory_region_variant,upstream_gene_variant | null | null | null | null | null | null | null | null | null | 31,765 | 147,196 | 0.215801 | 0.215801 | 31,765 |
1 | 138,551 | G | C | Rare | gnomAD | downstream_gene_variant,intron_variant&non_coding_transcript_variant,non_coding_transcript_exon_variant,regulatory_region_variant,upstream_gene_variant | null | null | null | null | null | null | null | null | null | 1 | 152,046 | 0.000007 | 0.000007 | 1 |
1 | 138,593 | G | T | Common | gnomAD | downstream_gene_variant,intron_variant&non_coding_transcript_variant,non_coding_transcript_exon_variant,regulatory_region_variant,upstream_gene_variant | null | null | null | null | null | null | null | null | null | 15,764 | 149,200 | 0.105657 | 0.105657 | 15,764 |
1 | 139,213 | A | G | Common | gnomAD | TF_binding_site_variant,downstream_gene_variant,intron_variant&non_coding_transcript_variant,non_coding_transcript_exon_variant,regulatory_region_variant,upstream_gene_variant | null | null | null | null | null | null | null | null | null | 42,485 | 144,294 | 0.294434 | 0.294434 | 42,485 |
1 | 139,233 | C | A | Common | gnomAD | TF_binding_site_variant,downstream_gene_variant,intron_variant&non_coding_transcript_variant,non_coding_transcript_exon_variant,regulatory_region_variant,upstream_gene_variant | null | null | null | null | null | null | null | null | null | 42,504 | 144,312 | 0.294529 | 0.294529 | 42,504 |
1 | 139,308 | G | T | Rare | gnomAD | downstream_gene_variant,intron_variant&non_coding_transcript_variant,non_coding_transcript_exon_variant,regulatory_region_variant,upstream_gene_variant | null | null | null | null | null | null | null | null | null | 1 | 152,022 | 0.000007 | 0.000007 | 1 |
1 | 181,512 | C | T | Rare | gnomAD | downstream_gene_variant,intron_variant&non_coding_transcript_variant,upstream_gene_variant | null | null | null | null | null | null | null | null | null | 1 | 148,886 | 0.000007 | 0.000007 | 1 |
1 | 181,930 | C | T | Rare | gnomAD | downstream_gene_variant,intron_variant&non_coding_transcript_variant,upstream_gene_variant | null | null | null | null | null | null | null | null | null | 1 | 150,830 | 0.000007 | 0.000007 | 1 |
1 | 181,967 | C | G | Rare | gnomAD | downstream_gene_variant,intron_variant&non_coding_transcript_variant,upstream_gene_variant | null | null | null | null | null | null | null | null | null | 1 | 151,214 | 0.000007 | 0.000007 | 1 |
1 | 183,040 | C | T | Rare | gnomAD | downstream_gene_variant,intron_variant&non_coding_transcript_variant,upstream_gene_variant | null | null | null | null | null | null | null | null | null | 1 | 142,786 | 0.000007 | 0.000007 | 1 |
1 | 183,473 | G | T | Rare | gnomAD | downstream_gene_variant,intron_variant&non_coding_transcript_variant,upstream_gene_variant | null | null | null | null | null | null | null | null | null | 1 | 151,774 | 0.000007 | 0.000007 | 1 |
1 | 184,360 | T | C | Rare | gnomAD | downstream_gene_variant,intron_variant&non_coding_transcript_variant,non_coding_transcript_exon_variant,upstream_gene_variant | null | null | null | null | null | null | null | null | null | 1 | 151,068 | 0.000007 | 0.000007 | 1 |
1 | 184,399 | T | C | Rare | gnomAD | downstream_gene_variant,intron_variant&non_coding_transcript_variant,non_coding_transcript_exon_variant,upstream_gene_variant | null | null | null | null | null | null | null | null | null | 1 | 151,496 | 0.000007 | 0.000007 | 1 |
1 | 187,009 | T | C | Rare | gnomAD | downstream_gene_variant,intron_variant&non_coding_transcript_variant,regulatory_region_variant | null | null | null | null | null | null | null | null | null | 1 | 152,094 | 0.000007 | 0.000007 | 1 |
1 | 189,448 | T | C | Rare | gnomAD | downstream_gene_variant,intron_variant&non_coding_transcript_variant,upstream_gene_variant | null | null | null | null | null | null | null | null | null | 1 | 152,146 | 0.000007 | 0.000007 | 1 |
1 | 190,661 | C | A | Rare | gnomAD | intron_variant&non_coding_transcript_variant,upstream_gene_variant | null | null | null | null | null | null | null | null | null | 1 | 151,408 | 0.000007 | 0.000007 | 1 |
1 | 190,946 | C | G | Rare | gnomAD | intron_variant&non_coding_transcript_variant,upstream_gene_variant | null | null | null | null | null | null | null | null | null | 1 | 152,240 | 0.000007 | 0.000007 | 1 |
1 | 191,471 | G | A | Rare | gnomAD | intron_variant&non_coding_transcript_variant,upstream_gene_variant | null | null | null | null | null | null | null | null | null | 1 | 152,284 | 0.000007 | 0.000007 | 1 |
1 | 191,773 | C | A | Rare | gnomAD | intron_variant&non_coding_transcript_variant,upstream_gene_variant | null | null | null | null | null | null | null | null | null | 1 | 152,246 | 0.000007 | 0.000007 | 1 |
1 | 191,790 | C | T | Rare | gnomAD | intron_variant&non_coding_transcript_variant,upstream_gene_variant | null | null | null | null | null | null | null | null | null | 1 | 152,246 | 0.000007 | 0.000007 | 1 |
1 | 264,499 | T | C | Rare | gnomAD | intron_variant&non_coding_transcript_variant,non_coding_transcript_exon_variant,upstream_gene_variant | null | null | null | null | null | null | null | null | null | 1 | 151,444 | 0.000007 | 0.000007 | 1 |
1 | 266,100 | C | T | Rare | gnomAD | intron_variant&non_coding_transcript_variant,non_coding_transcript_exon_variant,upstream_gene_variant | null | null | null | null | null | null | null | null | null | 1 | 146,614 | 0.000007 | 0.000007 | 1 |
1 | 267,585 | C | T | Rare | gnomAD | intron_variant&non_coding_transcript_variant,non_coding_transcript_exon_variant,regulatory_region_variant,upstream_gene_variant | null | null | null | null | null | null | null | null | null | 1 | 152,212 | 0.000007 | 0.000007 | 1 |
1 | 267,742 | T | A | Rare | gnomAD | TF_binding_site_variant,intron_variant&non_coding_transcript_variant,non_coding_transcript_exon_variant,regulatory_region_variant,upstream_gene_variant | null | null | null | null | null | null | null | null | null | 1 | 150,834 | 0.000007 | 0.000007 | 1 |
1 | 268,634 | G | C | Rare | gnomAD | intron_variant&non_coding_transcript_variant,non_coding_transcript_exon_variant,regulatory_region_variant,upstream_gene_variant | null | null | null | null | null | null | null | null | null | 1 | 152,124 | 0.000007 | 0.000007 | 1 |
1 | 269,178 | G | A | Rare | gnomAD | downstream_gene_variant,intron_variant&non_coding_transcript_variant,regulatory_region_variant,upstream_gene_variant | null | null | null | null | null | null | null | null | null | 1 | 152,222 | 0.000007 | 0.000007 | 1 |
1 | 269,184 | T | C | Rare | gnomAD | downstream_gene_variant,intron_variant&non_coding_transcript_variant,regulatory_region_variant,upstream_gene_variant | null | null | null | null | null | null | null | null | null | 1 | 152,204 | 0.000007 | 0.000007 | 1 |
1 | 269,228 | A | T | Rare | gnomAD | downstream_gene_variant,intron_variant&non_coding_transcript_variant,upstream_gene_variant | null | null | null | null | null | null | null | null | null | 1 | 151,982 | 0.000007 | 0.000007 | 1 |
1 | 269,283 | T | C | Rare | gnomAD | downstream_gene_variant,intron_variant&non_coding_transcript_variant,upstream_gene_variant | null | null | null | null | null | null | null | null | null | 1 | 152,046 | 0.000007 | 0.000007 | 1 |
1 | 270,731 | T | C | Rare | gnomAD | downstream_gene_variant,intron_variant&non_coding_transcript_variant,upstream_gene_variant | null | null | null | null | null | null | null | null | null | 1 | 152,000 | 0.000007 | 0.000007 | 1 |
1 | 270,936 | C | A | Rare | gnomAD | downstream_gene_variant,intron_variant&non_coding_transcript_variant,upstream_gene_variant | null | null | null | null | null | null | null | null | null | 1 | 149,508 | 0.000007 | 0.000007 | 1 |
1 | 271,359 | G | T | Rare | gnomAD | downstream_gene_variant,intron_variant&non_coding_transcript_variant,upstream_gene_variant | null | null | null | null | null | null | null | null | null | 1 | 150,762 | 0.000007 | 0.000007 | 1 |
1 | 274,143 | T | A | Rare | gnomAD | intron_variant&non_coding_transcript_variant | null | null | null | null | null | null | null | null | null | 1 | 151,344 | 0.000007 | 0.000007 | 1 |
1 | 278,389 | C | T | Rare | gnomAD | intron_variant&non_coding_transcript_variant | null | null | null | null | null | null | null | null | null | 1 | 152,100 | 0.000007 | 0.000007 | 1 |
1 | 283,047 | T | A | Rare | gnomAD | intron_variant&non_coding_transcript_variant | null | null | null | null | null | null | null | null | null | 1 | 152,300 | 0.000007 | 0.000007 | 1 |
1 | 286,723 | A | T | Rare | gnomAD | intron_variant&non_coding_transcript_variant | null | null | null | null | null | null | null | null | null | 1 | 144,050 | 0.000007 | 0.000007 | 1 |
1 | 286,747 | A | G | Common | gnomAD | intron_variant&non_coding_transcript_variant | null | null | null | null | null | null | null | null | null | 17,547 | 142,340 | 0.123275 | 0.123275 | 17,547 |
1 | 502,653 | G | T | Common | gnomAD | TF_binding_site_variant,downstream_gene_variant,intron_variant&non_coding_transcript_variant,non_coding_transcript_exon_variant,regulatory_region_variant,upstream_gene_variant | null | null | null | null | null | null | null | null | null | 12,969 | 149,076 | 0.086996 | 0.086996 | 12,969 |
1 | 505,171 | C | T | Rare | gnomAD | intron_variant&non_coding_transcript_variant,upstream_gene_variant | null | null | null | null | null | null | null | null | null | 1 | 151,476 | 0.000007 | 0.000007 | 1 |
1 | 605,658 | C | T | Rare | gnomAD | intron_variant,intron_variant&non_coding_transcript_variant | null | null | null | null | null | null | null | null | null | 1 | 141,710 | 0.000007 | 0.000007 | 1 |
1 | 608,783 | C | T | Rare | gnomAD | intron_variant,intron_variant&non_coding_transcript_variant | null | null | null | null | null | null | null | null | null | 1 | 142,484 | 0.000007 | 0.000007 | 1 |
1 | 632,597 | C | G | Rare | gnomAD | TF_binding_site_variant,downstream_gene_variant,intron_variant&non_coding_transcript_variant,non_coding_transcript_exon_variant,regulatory_region_variant,upstream_gene_variant | null | null | null | null | null | null | null | null | null | 1 | 141,786 | 0.000007 | 0.000007 | 1 |
1 | 656,707 | G | A | Rare | gnomAD | intron_variant&non_coding_transcript_variant | null | null | null | null | null | null | null | null | null | 1 | 145,854 | 0.000007 | 0.000007 | 1 |
1 | 667,417 | G | A | Rare | gnomAD | intron_variant&non_coding_transcript_variant | null | null | null | null | null | null | null | null | null | 1 | 141,792 | 0.000007 | 0.000007 | 1 |
1 | 701,359 | A | G | Rare | gnomAD | downstream_gene_variant,intron_variant,intron_variant&non_coding_transcript_variant,upstream_gene_variant | null | null | null | null | null | null | null | null | null | 1 | 149,804 | 0.000007 | 0.000007 | 1 |
1 | 701,384 | C | T | Rare | gnomAD | downstream_gene_variant,intron_variant,intron_variant&non_coding_transcript_variant,upstream_gene_variant | null | null | null | null | null | null | null | null | null | 1 | 149,646 | 0.000007 | 0.000007 | 1 |
1 | 701,585 | A | T | Rare | gnomAD | downstream_gene_variant,intron_variant,intron_variant&non_coding_transcript_variant,upstream_gene_variant | null | null | null | null | null | null | null | null | null | 1 | 150,304 | 0.000007 | 0.000007 | 1 |
1 | 702,400 | T | C | Rare | gnomAD | intron_variant,intron_variant&non_coding_transcript_variant,upstream_gene_variant | null | null | null | null | null | null | null | null | null | 1 | 150,474 | 0.000007 | 0.000007 | 1 |
1 | 727,242 | G | A | Common | gnomAD | downstream_gene_variant,intron_variant&non_coding_transcript_variant,non_coding_transcript_exon_variant,upstream_gene_variant | null | null | null | null | null | null | null | null | null | 22,212 | 142,898 | 0.15544 | 0.15544 | 22,212 |
1 | 730,801 | G | A | Rare | gnomAD | downstream_gene_variant,intron_variant&non_coding_transcript_variant,regulatory_region_variant,upstream_gene_variant | null | null | null | null | null | null | null | null | null | 1 | 151,170 | 0.000007 | 0.000007 | 1 |
1 | 734,220 | G | A | Rare | gnomAD | downstream_gene_variant,intron_variant,intron_variant&non_coding_transcript_variant,regulatory_region_variant,upstream_gene_variant | null | null | null | null | null | null | null | null | null | 1 | 145,906 | 0.000007 | 0.000007 | 1 |
1 | 736,852 | C | T | Common | gnomAD | downstream_gene_variant,intron_variant,intron_variant&non_coding_transcript_variant,upstream_gene_variant | null | null | null | null | null | null | null | null | null | 11,218 | 149,074 | 0.075251 | 0.075251 | 11,218 |
1 | 737,549 | G | A | Rare | gnomAD | downstream_gene_variant,intron_variant,intron_variant&non_coding_transcript_variant,regulatory_region_variant,upstream_gene_variant | null | null | null | null | null | null | null | null | null | 1 | 152,156 | 0.000007 | 0.000007 | 1 |
1 | 739,119 | A | G | Rare | gnomAD | downstream_gene_variant,intron_variant,intron_variant&non_coding_transcript_variant,upstream_gene_variant | null | null | null | null | null | null | null | null | null | 1 | 150,322 | 0.000007 | 0.000007 | 1 |
1 | 757,731 | C | T | Rare | gnomAD | downstream_gene_variant,intron_variant&non_coding_transcript_variant,upstream_gene_variant | null | null | null | null | null | null | null | null | null | 1 | 149,702 | 0.000007 | 0.000007 | 1 |
1 | 758,351 | A | G | Common | gnomAD | intron_variant&non_coding_transcript_variant,upstream_gene_variant | null | null | null | null | null | null | null | null | null | 22,614 | 147,596 | 0.153216 | 0.153216 | 22,614 |
1 | 758,443 | G | C | Common | gnomAD | intron_variant&non_coding_transcript_variant,upstream_gene_variant | null | null | null | null | null | null | null | null | null | 23,465 | 149,308 | 0.157158 | 0.157158 | 23,465 |
1 | 762,385 | C | T | Rare | gnomAD | downstream_gene_variant,intron_variant&non_coding_transcript_variant,upstream_gene_variant | null | null | null | null | null | null | null | null | null | 1 | 151,058 | 0.000007 | 0.000007 | 1 |
1 | 762,483 | A | G | Rare | gnomAD | downstream_gene_variant,intron_variant&non_coding_transcript_variant,upstream_gene_variant | null | null | null | null | null | null | null | null | null | 1 | 147,226 | 0.000007 | 0.000007 | 1 |
1 | 767,625 | G | T | Rare | gnomAD | intron_variant&non_coding_transcript_variant | null | null | null | null | null | null | null | null | null | 1 | 146,596 | 0.000007 | 0.000007 | 1 |
1 | 770,036 | C | T | Rare | gnomAD | intron_variant&non_coding_transcript_variant | null | null | null | null | null | null | null | null | null | 1 | 151,946 | 0.000007 | 0.000007 | 1 |
1 | 770,352 | G | C | Rare | gnomAD | intron_variant&non_coding_transcript_variant | null | null | null | null | null | null | null | null | null | 1 | 151,696 | 0.000007 | 0.000007 | 1 |
1 | 770,502 | G | A | Common | gnomAD | intron_variant&non_coding_transcript_variant | null | null | null | null | null | null | null | null | null | 7,838 | 145,076 | 0.054027 | 0.054027 | 7,838 |
1 | 771,265 | A | C | Common | gnomAD | intron_variant&non_coding_transcript_variant | null | null | null | null | null | null | null | null | null | 11,879 | 151,090 | 0.078622 | 0.078622 | 11,879 |
1 | 774,855 | T | A | Rare | gnomAD | intron_variant&non_coding_transcript_variant,upstream_gene_variant | null | null | null | null | null | null | null | null | null | 1 | 151,956 | 0.000007 | 0.000007 | 1 |
1 | 775,103 | G | A | Rare | gnomAD | intron_variant&non_coding_transcript_variant,upstream_gene_variant | null | null | null | null | null | null | null | null | null | 1 | 151,516 | 0.000007 | 0.000007 | 1 |
1 | 775,930 | G | A | Common | gnomAD | intron_variant&non_coding_transcript_variant,upstream_gene_variant | null | null | null | null | null | null | null | null | null | 17,271 | 140,674 | 0.122773 | 0.122773 | 17,271 |
1 | 776,357 | G | C | Rare | gnomAD | intron_variant&non_coding_transcript_variant,upstream_gene_variant | null | null | null | null | null | null | null | null | null | 1 | 151,984 | 0.000007 | 0.000007 | 1 |
1 | 776,848 | G | T | Rare | gnomAD | intron_variant&non_coding_transcript_variant,upstream_gene_variant | null | null | null | null | null | null | null | null | null | 1 | 150,722 | 0.000007 | 0.000007 | 1 |
1 | 777,826 | G | T | Rare | gnomAD | intron_variant&non_coding_transcript_variant,regulatory_region_variant,upstream_gene_variant | null | null | null | null | null | null | null | null | null | 1 | 151,896 | 0.000007 | 0.000007 | 1 |
1 | 777,847 | T | C | Rare | gnomAD | intron_variant&non_coding_transcript_variant,regulatory_region_variant,upstream_gene_variant | null | null | null | null | null | null | null | null | null | 1 | 151,994 | 0.000007 | 0.000007 | 1 |
1 | 777,913 | C | T | Rare | gnomAD | intron_variant&non_coding_transcript_variant,regulatory_region_variant,upstream_gene_variant | null | null | null | null | null | null | null | null | null | 1 | 151,828 | 0.000007 | 0.000007 | 1 |
1 | 777,979 | G | A | Rare | gnomAD | intron_variant&non_coding_transcript_variant,regulatory_region_variant,upstream_gene_variant | null | null | null | null | null | null | null | null | null | 1 | 152,146 | 0.000007 | 0.000007 | 1 |
1 | 778,304 | T | G | Rare | gnomAD | TF_binding_site_variant,intron_variant&non_coding_transcript_variant,non_coding_transcript_exon_variant,regulatory_region_variant,upstream_gene_variant | null | null | null | null | null | null | null | null | null | 1 | 152,216 | 0.000007 | 0.000007 | 1 |
1 | 778,639 | A | G | Common | gnomAD | TF_binding_site_variant,intron_variant&non_coding_transcript_variant,non_coding_transcript_exon_variant,regulatory_region_variant,upstream_gene_variant | null | null | null | null | null | null | null | null | null | 19,303 | 150,884 | 0.127933 | 0.127933 | 19,303 |
1 | 779,047 | G | A | Common | gnomAD | TF_binding_site_variant,intron_variant&non_coding_transcript_variant,non_coding_transcript_exon_variant,regulatory_region_variant,upstream_gene_variant | null | null | null | null | null | null | null | null | null | 124,540 | 151,914 | 0.819806 | 0.180194 | 27,374 |
1 | 779,196 | G | C | Rare | gnomAD | intron_variant&non_coding_transcript_variant,regulatory_region_variant,upstream_gene_variant | null | null | null | null | null | null | null | null | null | 1 | 152,154 | 0.000007 | 0.000007 | 1 |
1 | 779,827 | T | G | Rare | gnomAD | intron_variant&non_coding_transcript_variant,regulatory_region_variant,upstream_gene_variant | null | null | null | null | null | null | null | null | null | 1 | 152,194 | 0.000007 | 0.000007 | 1 |
1 | 780,149 | T | C | Rare | gnomAD | intron_variant&non_coding_transcript_variant,regulatory_region_variant,upstream_gene_variant | null | null | null | null | null | null | null | null | null | 1 | 152,210 | 0.000007 | 0.000007 | 1 |
1 | 780,574 | G | T | Rare | gnomAD | intron_variant&non_coding_transcript_variant,regulatory_region_variant,upstream_gene_variant | null | null | null | null | null | null | null | null | null | 1 | 150,846 | 0.000007 | 0.000007 | 1 |
1 | 780,633 | T | C | Rare | gnomAD | intron_variant&non_coding_transcript_variant,regulatory_region_variant,upstream_gene_variant | null | null | null | null | null | null | null | null | null | 1 | 151,798 | 0.000007 | 0.000007 | 1 |
1 | 780,807 | A | G | Rare | gnomAD | intron_variant&non_coding_transcript_variant,regulatory_region_variant,upstream_gene_variant | null | null | null | null | null | null | null | null | null | 1 | 152,004 | 0.000007 | 0.000007 | 1 |
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Human variants
A curated set of variants from three sources: ClinVar, COSMIC, OMIM and gnomAD. Predictions for methods benchmarked in GPN-MSA paper can be downloaded from here. Functional annotations can be downloaded from here.
For more information check out our paper and repository.
Data sources
ClinVar: Missense variants considered "Pathogenic" by human labelers.
COSMIC: Somatic missense variants with a frequency at least 0.1% in cancer samples (whole-genome and whole-exome sequencing only).
OMIM: Regulatory variants considered "Pathogenic" by human labelers, curated in this paper.
gnomAD: All common variants (MAF > 5%) as well as an equally-sized subset of rare variants (MAC=1). Only autosomes are included.
Usage
from datasets import load_dataset
dataset = load_dataset("songlab/human_variants", split="test")
Subset - ClinVar Pathogenic vs. gnomAD common (missense) (can specify num_proc to speed up):
dataset = dataset.filter(lambda v: v["source"]=="ClinVar" or (v["label"]=="Common" and "missense" in v["consequence"]))
Subset - COSMIC frequent vs. gnomAD common (missense):
dataset = dataset.filter(lambda v: v["source"]=="COSMIC" or (v["label"]=="Common" and "missense" in v["consequence"]))
Subset - OMIM Pathogenic vs. gnomAD common (regulatory):
cs = ["5_prime_UTR", "upstream_gene", "intergenic", "3_prime_UTR", "non_coding_transcript_exon"]
dataset = dataset.filter(lambda v: v["source"]=="OMIM" or (v["label"]=="Common" and "missense" not in v["consequence"] and any([c in v["consequence"] for c in cs])))
Subset - gnomAD rare vs. gnomAD common:
dataset = dataset.filter(lambda v: v["source"]=="gnomAD")
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