del[SNPCLASS] - SNP

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Select item 164451.

rs16445 [Homo sapiens]

Variant type:: DEL
Alleles:: CT>- [Show Flanks]
Chromosome:: 22:49903387 (GRCh38)
22:50297035 (GRCh37)
Canonical SPDI:: NC_000022.11:49903386:CT:
Gene:: ALG12 (Varview)
Functional Consequence:: intron_variant,3_prime_UTR_variant
Clinical significance:: likely-benign
Validated:: by frequency,by alfa,by cluster
MAF:: -=0.098044/2697 (ALFA)
-=0.046729/10 (Vietnamese)
-=0.053613/899 (TOMMO)
-=0.064022/321 (1000Genomes)
-=0.070362/18624 (TOPMED)
-=0.07645/10718 (GnomAD)
-=0.092535/12704 (GnomAD_exomes)
-=0.101972/393 (ALSPAC)
-=0.103206/103 (GoNL)
-=0.105448/391 (TWINSUK)
-=0.114069/1547 (ExAC)
-=0.146667/88 (NorthernSweden)
-=0.153795/689 (Estonian)
-=0.2/8 (GENOME_DK)
HGVS:: NC_000022.11:g.49903387_49903388del, NC_000022.10:g.50297035_50297036del, NG_008927.1:g.20071_20072del, NM_024105.4:c.*450_*451del, NM_024105.3:c.*450_*451del

Select item 1339002.

rs133900 [Homo sapiens]

Variant type:: DEL
Alleles:: T>- [Show Flanks]
Chromosome:: 22:25767857 (GRCh38)
22:26163824 (GRCh37)
Canonical SPDI:: NC_000022.11:25767856:T:
Gene:: MYO18B (Varview)
Functional Consequence:: intron_variant,genic_upstream_transcript_variant
Clinical significance:: benign
Validated:: by frequency,by alfa,by cluster
MAF:: -=0.057704/737 (ALFA)
-=0.095017/1592 (TOMMO)
-=0.129808/27 (Vietnamese)
-=0.129913/238 (Korea1K)
-=0.16317/731 (Estonian)
-=0.187695/940 (1000Genomes)
-=0.191667/115 (NorthernSweden)
-=0.194344/749 (ALSPAC)
-=0.203407/203 (GoNL)
-=0.209817/778 (TWINSUK)
-=0.218844/30650 (GnomAD)
-=0.223235/59088 (TOPMED)
-=0.225/9 (GENOME_DK)
HGVS:: NC_000022.11:g.25767857del, NC_000022.10:g.26163824del, NG_046772.1:g.30714del

Select item 17997703.

rs1799770 [Homo sapiens]

Variant type:: DEL
Alleles:: A>- [Show Flanks]
Chromosome:: 1:156879118 (GRCh38)
1:156848910 (GRCh37)
Canonical SPDI:: NC_000001.11:156879117:A:
Gene:: NTRK1 (Varview)
Functional Consequence:: intron_variant
Clinical significance:: benign,benign-likely-benign
Validated:: by frequency,by alfa,by cluster
MAF:: -=0.030554/799 (ALFA)
-=0.03058/137 (Estonian)
-=0.035/21 (NorthernSweden)
-=0.043086/43 (GoNL)
-=0.045619/765 (TOMMO)
-=0.047483/183 (ALSPAC)
-=0.050431/187 (TWINSUK)
-=0.059322/14732 (GnomAD_exomes)
-=0.0625/7482 (ExAC)
-=0.063161/8852 (GnomAD)
-=0.066048/121 (Korea1K)
-=0.066704/835 (GoESP)
-=0.066886/17704 (TOPMED)
-=0.08807/441 (1000Genomes)
-=0.1/4 (GENOME_DK)
HGVS:: NC_000001.11:g.156879118del, NC_000001.10:g.156848910del, NG_007493.1:g.68369del

PubMed

Select item 20667344.

rs2066734 [Homo sapiens]

Variant type:: DEL
Alleles:: AA>- [Show Flanks]
Chromosome:: 11:108227733 (GRCh38)
11:108098460 (GRCh37)
Canonical SPDI:: NC_000011.10:108227732:AA:
Gene:: ATM (Varview)
Functional Consequence:: intron_variant,genic_upstream_transcript_variant
Clinical significance:: benign
Validated:: by frequency,by alfa,by cluster
MAF:: -=0.405663/11189 (ALFA)
-=0.320755/68 (Vietnamese)
-=0.333333/200 (NorthernSweden)
-=0.335784/4202 (GoESP)
-=0.352572/49303 (GnomAD)
-=0.360153/95329 (TOPMED)
-=0.37664/1886 (1000Genomes)
-=0.395003/6619 (TOMMO)
-=0.395536/1772 (Estonian)
-=0.411572/754 (Korea1K)
-=0.413828/413 (GoNL)
-=0.420173/1558 (TWINSUK)
-=0.422159/1627 (ALSPAC)
-=0.425343/51583 (ExAC)
-=0.43522/109355 (GnomAD_exomes)
-=0.475/19 (GENOME_DK)
HGVS:: NC_000011.10:g.108227733_108227734del, NC_000011.9:g.108098460_108098461del, NG_009830.1:g.9902_9903del

PubMed

Select item 22275745.

rs2227574 [Homo sapiens]

Variant type:: DEL
Alleles:: G>- [Show Flanks]
Chromosome:: 10:73917409 (GRCh38)
10:75677167 (GRCh37)
Canonical SPDI:: NC_000010.11:73917408:G:
Gene:: PLAU (Varview), C10orf55 (Varview)
Functional Consequence:: 3_prime_UTR_variant,intron_variant
Clinical significance:: benign
Validated:: by frequency,by alfa,by cluster
MAF:: -=0.370778/3469 (ALFA)
-=0.098131/21 (Vietnamese)
-=0.110765/1856 (TOMMO)
-=0.110808/203 (Korea1K)
-=0.370706/1856 (1000Genomes)
G=0.417745/1549 (TWINSUK)
G=0.43617/1681 (ALSPAC)
G=0.437876/437 (GoNL)
G=0.45/18 (GENOME_DK)
G=0.453333/272 (NorthernSweden)
G=0.490714/68697 (GnomAD)
-=0.497321/2228 (Estonian)
-=0.499875/132312 (TOPMED)
HGVS:: NC_000010.11:g.73917409del, NC_000010.10:g.75677167del, NG_011904.1:g.11306del, NM_002658.6:c.*844del, NM_002658.5:c.*844del, NM_002658.4:c.*844del, NM_002658.3:c.*844del, NM_001145031.3:c.*844del, NM_001145031.2:c.*844del, NM_001145031.1:c.*844del, NM_001319191.2:c.*844del, NM_001319191.1:c.*844del, XM_011539866.3:c.*844del, XM_011539866.2:c.*844del, XM_011539866.1:c.*844del, XM_047425353.1:c.*844del

Select item 23074346.

rs2307434 [Homo sapiens]

Variant type:: DEL
Alleles:: G>- [Show Flanks]
Chromosome:: 15:89326743 (GRCh38)
15:89869974 (GRCh37)
Canonical SPDI:: NC_000015.10:89326742:G:
Gene:: POLG (Varview), MIR6766 (Varview)
Functional Consequence:: non_coding_transcript_variant,intron_variant
Clinical significance:: likely-benign,benign
Validated:: by frequency,by alfa,by cluster
MAF:: -=0.000272/12 (ALFA)
-=0.002372/596 (GnomAD_exomes)
-=0.002887/350 (ExAC)
-=0.00891/1249 (GnomAD)
-=0.009437/2498 (TOPMED)
-=0.009986/125 (GoESP)
-=0.016396/82 (1000Genomes)
HGVS:: NC_000015.10:g.89326743del, NC_000015.9:g.89869974del, NG_008218.2:g.13053del, NR_106824.1:n.68del

Select item 23080007.

rs2308000 [Homo sapiens]

Variant type:: DEL
Alleles:: CTT>- [Show Flanks]
Chromosome:: 5:7871151 (GRCh38)
5:7871264 (GRCh37)
Canonical SPDI:: NC_000005.10:7871150:CTT:
Gene:: MTRR (Varview)
Functional Consequence:: intron_variant
Clinical significance:: benign
Validated:: by frequency,by alfa,by cluster
MAF:: CTT=0.466901/8647 (ALFA)
-=0.370691/6213 (TOMMO)
-=0.386792/82 (Vietnamese)
-=0.395197/724 (Korea1K)
CTT=0.416922/110355 (TOPMED)
CTT=0.431015/60212 (GnomAD)
CTT=0.445971/2233 (1000Genomes)
-=0.471875/2114 (Estonian)
-=0.473333/284 (NorthernSweden)
-=0.488064/1881 (ALSPAC)
-=0.492988/1828 (TWINSUK)
-=0.497996/497 (GoNL)
CTT=0.5/20 (GENOME_DK)
HGVS:: NC_000005.10:g.7871151_7871153del, NC_000005.9:g.7871264_7871266del, NG_008856.1:g.7048_7050del, NG_033101.1:g.2885_2887del

Select item 30315058.

rs3031505 [Homo sapiens]

Variant type:: DEL
Alleles:: AAACT>- [Show Flanks]
Chromosome:: 10:29495056 (GRCh38)
10:29783985 (GRCh37)
Canonical SPDI:: NC_000010.11:29495055:AAACT:
Gene:: SVIL (Varview)
Functional Consequence:: intron_variant
Clinical significance:: benign
Validated:: by frequency,by alfa,by cluster
MAF:: AAACT=0.258625/4243 (ALFA)
-=0.11032/5683 (ExAC)
-=0.224251/25988 (GnomAD_exomes)
-=0.242538/2844 (GoESP)
AAACT=0.282115/4728 (TOMMO)
AAACT=0.288882/1447 (1000Genomes)
HGVS:: NC_000010.11:g.29495056_29495060del, NC_000010.10:g.29783985_29783989del, NG_033998.1:g.245742_245746del

Select item 30484889.

rs3048488 [Homo sapiens]

Variant type:: DEL
Alleles:: AT>- [Show Flanks]
Chromosome:: 1:67049881 (GRCh38)
1:67515564 (GRCh37)
Canonical SPDI:: NC_000001.11:67049880:AT:
Gene:: SLC35D1 (Varview)
Functional Consequence:: intron_variant
Clinical significance:: benign
Validated:: by frequency,by alfa,by cluster
MAF:: -=0.03292/908 (ALFA)
-=0.01/6 (NorthernSweden)
-=0.019038/19 (GoNL)
-=0.021036/78 (TWINSUK)
-=0.024131/93 (ALSPAC)
-=0.026215/328 (GoESP)
-=0.032689/4582 (GnomAD)
-=0.040625/182 (Estonian)
-=0.041925/11097 (TOPMED)
-=0.059299/14065 (GnomAD_exomes)
-=0.062224/6032 (ExAC)
-=0.072299/362 (1000Genomes)
-=0.154206/33 (Vietnamese)
-=0.210064/3521 (TOMMO)
HGVS:: NC_000001.11:g.67049881_67049882del, NC_000001.10:g.67515564_67515565del, NG_012933.1:g.9516_9517del

Select item 305162110.

rs3051621 [Homo sapiens]

Variant type:: DEL
Alleles:: AT>- [Show Flanks]
Chromosome:: 5:127418050 (GRCh38)
5:126753742 (GRCh37)
Canonical SPDI:: NC_000005.10:127418049:AT:
Gene:: MEGF10 (Varview)
Functional Consequence:: intron_variant
Clinical significance:: likely-benign
Validated:: by frequency,by alfa,by cluster
MAF:: -=0.015389/285 (ALFA)
-=0.014934/3953 (TOPMED)
-=0.016/2243 (GnomAD)
-=0.018339/68 (TWINSUK)
-=0.020089/90 (Estonian)
-=0.021796/84 (ALSPAC)
-=0.023333/14 (NorthernSweden)
-=0.024048/24 (GoNL)
-=0.0287/481 (TOMMO)
-=0.031699/159 (1000Genomes)
-=0.034934/64 (Korea1K)
-=0.04717/10 (Vietnamese)
-=0.05/2 (GENOME_DK)
HGVS:: NC_000005.10:g.127418050_127418051del, NC_000005.9:g.126753742_126753743del, NG_032072.2:g.132287_132288del

Select item 305170211.

rs3051702 [Homo sapiens]

Variant type:: DEL
Alleles:: TG>- [Show Flanks]
Chromosome:: 18:62112984 (GRCh38)
18:59780217 (GRCh37)
Canonical SPDI:: NC_000018.10:62112983:TG:
Gene:: PIGN (Varview)
Functional Consequence:: intron_variant
Clinical significance:: benign
Validated:: by frequency,by alfa,by cluster
MAF:: -=0.096253/1572 (ALFA)
-=0.070093/15 (Vietnamese)
-=0.073333/44 (NorthernSweden)
-=0.0804/21281 (TOPMED)
-=0.081369/11389 (GnomAD)
-=0.0901/451 (1000Genomes)
-=0.094188/94 (GoNL)
-=0.101194/390 (ALSPAC)
-=0.107066/397 (TWINSUK)
-=0.1125/504 (Estonian)
-=0.114083/209 (Korea1K)
-=0.115472/1935 (TOMMO)
-=0.175/7 (GENOME_DK)
HGVS:: NC_000018.10:g.62112984_62112985del, NC_000018.9:g.59780217_59780218del, NG_033144.1:g.79072_79073del

Select item 305845812.

rs3058458 [Homo sapiens]

Variant type:: DEL
Alleles:: AGAG>- [Show Flanks]
Chromosome:: 5:74726281 (GRCh38)
5:74022106 (GRCh37)
Canonical SPDI:: NC_000005.10:74726280:AGAG:
Gene:: GFM2 (Varview)
Functional Consequence:: genic_downstream_transcript_variant,intron_variant
Clinical significance:: benign
Validated:: by frequency,by alfa,by cluster
MAF:: -=0.029184/422 (ALFA)
-=0.006795/114 (TOMMO)
-=0.009346/2 (Vietnamese)
-=0.014738/27 (Korea1K)
-=0.075/3 (GENOME_DK)
-=0.088333/53 (NorthernSweden)
-=0.094866/425 (Estonian)
-=0.125584/484 (ALSPAC)
-=0.127255/127 (GoNL)
-=0.132147/490 (TWINSUK)
-=0.145222/727 (1000Genomes)
-=0.164395/22986 (GnomAD)
-=0.168167/44512 (TOPMED)
HGVS:: NC_000005.10:g.74726281_74726284del, NC_000005.9:g.74022106_74022109del, NG_011531.1:g.45934_45937del

Select item 308742613.

rs3087426 [Homo sapiens]

Variant type:: DEL
Alleles:: G>- [Show Flanks]
Chromosome:: 8:31141365 (GRCh38)
8:30998881 (GRCh37)
Canonical SPDI:: NC_000008.11:31141364:G:
Gene:: WRN (Varview)
Functional Consequence:: intron_variant
Clinical significance:: benign
Validated:: by frequency,by alfa,by cluster
MAF:: -=0.021963/333 (ALFA)
-=0.024878/417 (TOMMO)
-=0.025655/47 (Korea1K)
-=0.037383/8 (Vietnamese)
-=0.043333/26 (NorthernSweden)
-=0.047626/239 (1000Genomes)
-=0.052118/13795 (TOPMED)
-=0.055272/7751 (GnomAD)
-=0.064995/241 (TWINSUK)
-=0.067981/262 (ALSPAC)
-=0.068136/68 (GoNL)
-=0.073214/328 (Estonian)
-=0.125/5 (GENOME_DK)
HGVS:: NC_000008.11:g.31141365del, NC_000008.10:g.30998881del, NG_008870.1:g.113104del

Select item 313636114.

rs3136361 [Homo sapiens]

Variant type:: DEL
Alleles:: ATAAAAGGTGATATT>- [Show Flanks]
Chromosome:: 2:47805861 (GRCh38)
2:48033000 (GRCh37)
Canonical SPDI:: NC_000002.12:47805860:ATAAAAGGTGATATT:
Gene:: MSH6 (Varview)
Functional Consequence:: intron_variant
Clinical significance:: benign
Validated:: by frequency,by alfa,by cluster
MAF:: -=0.021666/257 (ALFA)
-=0./0 (TWINSUK)
-=0.000106/2 (TOMMO)
-=0.000259/1 (ALSPAC)
-=0.000546/1 (Korea1K)
-=0.024792/3476 (GnomAD)
-=0.026546/133 (1000Genomes)
HGVS:: NC_000002.12:g.47805861_47805875del, NC_000002.11:g.48033000_48033014del, NG_008397.1:g.104801_104815del, NG_007111.1:g.27715_27729del

Select item 321201815.

rs3212018 [Homo sapiens]

Variant type:: DEL
Alleles:: GCACAAATAAAGCACT>- [Show Flanks]
Chromosome:: 7:80674385 (GRCh38)
7:80303701 (GRCh37)
Canonical SPDI:: NC_000007.14:80674384:GCACAAATAAAGCACT:
Gene:: CD36 (Varview)
Functional Consequence:: non_coding_transcript_variant,intron_variant,3_prime_UTR_variant
Clinical significance:: benign
Validated:: by frequency,by alfa,by cluster
MAF:: -=0.1379/3028 (ALFA)
-=0.053755/901 (TOMMO)
-=0.070755/15 (Vietnamese)
-=0.08679/159 (Korea1K)
-=0.090568/580 (1000Genomes)
-=0.10558/27946 (TOPMED)
-=0.114326/16007 (GnomAD)
-=0.131552/507 (ALSPAC)
-=0.138333/83 (NorthernSweden)
-=0.138619/514 (TWINSUK)
-=0.204241/915 (Estonian)
HGVS:: NC_000007.14:g.80674385_80674400del, NC_000007.13:g.80303701_80303716del, NG_008192.1:g.77198_77213del, NM_000072.3:c.*238_*253del, NM_001001547.3:c.*238_*253del, NM_001001547.2:c.*238_*253del, NM_001127444.2:c.*238_*253del, NM_001127444.1:c.*238_*253del, NM_001127443.2:c.*238_*253del, NM_001127443.1:c.*238_*253del, NM_001289911.2:c.*238_*253del, NM_001289911.1:c.*238_*253del, NM_001371081.1:c.*238_*253del, NM_001371074.1:c.*238_*253del, NM_001371078.1:c.*238_*253del, NM_001371079.1:c.*238_*253del, NM_001289909.1:c.*238_*253del, NR_110501.1:n.1648_1663del, NM_001289908.1:c.*238_*253del, NM_001371080.1:c.*238_*253del

PubMed

Select item 321235116.

rs3212351 [Homo sapiens]

Variant type:: DEL
Alleles:: AT>- [Show Flanks]
Chromosome:: 16:89917680 (GRCh38)
16:89984088 (GRCh37)
Canonical SPDI:: NC_000016.10:89917679:AT:
Gene:: MC1R (Varview), LOC124903759 (Varview)
Functional Consequence:: intron_variant,2KB_upstream_variant,upstream_transcript_variant
Clinical significance:: benign
Validated:: by frequency,by alfa,by cluster
MAF:: -=0.345896/6406 (ALFA)
AT=0.192052/3219 (TOMMO)
AT=0.2369/434 (Korea1K)
-=0.303128/1124 (TWINSUK)
-=0.305916/1179 (ALSPAC)
-=0.315631/315 (GoNL)
-=0.325/13 (GENOME_DK)
-=0.331696/1486 (Estonian)
-=0.376465/52666 (GnomAD)
-=0.38/228 (NorthernSweden)
-=0.391601/103653 (TOPMED)
AT=0.448113/95 (Vietnamese)
-=0.480325/2405 (1000Genomes)
HGVS:: NC_000016.10:g.89917680_89917681del, NC_000016.9:g.89984088_89984089del, NG_027810.1:g.672_673del, NG_012026.1:g.4802_4803del

PubMed

Select item 321407417.

rs3214074 [Homo sapiens]

Variant type:: DEL
Alleles:: A>- [Show Flanks]
Chromosome:: 21:44287633 (GRCh38)
21:45707516 (GRCh37)
Canonical SPDI:: NC_000021.9:44287632:A:
Gene:: AIRE (Varview)
Functional Consequence:: intron_variant
Clinical significance:: benign
Validated:: by frequency,by alfa,by cluster
MAF:: -=0.007942/209 (ALFA)
-=0.000519/2 (ALSPAC)
-=0.001079/4 (TWINSUK)
-=0.006667/4 (NorthernSweden)
-=0.010045/45 (Estonian)
-=0.050859/906 (ExAC)
-=0.05318/8049 (GnomAD_exomes)
-=0.06371/744 (GoESP)
-=0.069776/9778 (GnomAD)
-=0.080751/21374 (TOPMED)
-=0.135072/865 (1000Genomes)
-=0.30671/5140 (TOMMO)
-=0.341121/73 (Vietnamese)
-=0.402293/737 (Korea1K)
HGVS:: NC_000021.9:g.44287633del, NC_000021.8:g.45707516del, NG_009556.1:g.6754del

Select item 321413918.

rs3214139 [Homo sapiens]

Variant type:: DEL
Alleles:: C>- [Show Flanks]
Chromosome:: X:13719810 (GRCh38)
X:13737929 (GRCh37)
Canonical SPDI:: NC_000023.11:13719809:C:
Gene:: TRAPPC2 (Varview), OFD1 (Varview)
Functional Consequence:: intron_variant,genic_upstream_transcript_variant
Clinical significance:: benign
Validated:: by frequency,by alfa,by cluster
MAF:: -=0.386617/3952 (ALFA)
C=0.333333/16 (Vietnamese)
C=0.365661/1380 (1000Genomes)
C=0.375/15 (GENOME_DK)
C=0.379309/4871 (TOMMO)
C=0.405784/107407 (TOPMED)
C=0.410523/1186 (ALSPAC)
C=0.41343/1533 (TWINSUK)
HGVS:: NC_000023.11:g.13719810del, NC_000023.10:g.13737929del, NG_011555.1:g.19814del

Select item 321426419.

rs3214264 [Homo sapiens]

Variant type:: DEL
Alleles:: C>- [Show Flanks]
Chromosome:: 12:1792577 (GRCh38)
12:1901743 (GRCh37)
Canonical SPDI:: NC_000012.12:1792576:C:
Gene:: CACNA2D4 (Varview)
Functional Consequence:: 3_prime_UTR_variant,genic_downstream_transcript_variant
Clinical significance:: likely-benign
Validated:: by frequency,by alfa,by cluster
MAF:: -=0.007114/130 (ALFA)
-=0.002697/10 (TWINSUK)
-=0.003373/13 (ALSPAC)
-=0.004008/4 (GoNL)
-=0.018833/4985 (TOPMED)
-=0.021205/95 (Estonian)
-=0.021228/2963 (GnomAD)
-=0.025/1 (GENOME_DK)
-=0.026667/16 (NorthernSweden)
-=0.035603/178 (1000Genomes)
-=0.055068/923 (TOMMO)
-=0.084607/155 (Korea1K)
HGVS:: NC_000012.12:g.1792577del, NC_000012.11:g.1901743del, NG_012663.2:g.131128del, NM_172364.5:c.*1078del, NM_172364.4:c.*1078del, NW_018654718.1:g.134721del, NM_001005766.1:c.*1078del, NM_001005737.1:c.*1685del

Select item 321428520.

rs3214285 [Homo sapiens]

Variant type:: DEL
Alleles:: AG>- [Show Flanks]
Chromosome:: 17:68540072 (GRCh38)
17:66536213 (GRCh37)
Canonical SPDI:: NC_000017.11:68540071:AG:
Gene:: PRKAR1A (Varview), FAM20A (Varview)
Functional Consequence:: non_coding_transcript_variant,intron_variant,genic_downstream_transcript_variant
Clinical significance:: benign
Validated:: by frequency,by alfa,by cluster
MAF:: -=0.225594/4178 (ALFA)
-=0.11215/24 (Vietnamese)
-=0.173035/317 (Korea1K)
-=0.205/123 (NorthernSweden)
-=0.208701/55241 (TOPMED)
-=0.209713/1050 (1000Genomes)
-=0.212247/818 (ALSPAC)
-=0.215052/30100 (GnomAD)
-=0.230313/854 (TWINSUK)
-=0.232465/232 (GoNL)
-=0.25067/1123 (Estonian)
-=0.298818/5008 (TOMMO)
HGVS:: NC_000017.11:g.68540072_68540073del, NC_000017.10:g.66536213_66536214del, NG_007093.3:g.131450_131451del, NG_029809.1:g.65882_65883del, XR_934487.4:n.2482_2483del, XR_934487.1:n.1909_1910del

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