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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 |
End of preview. Expand
in Data Studio
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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