{"id":13348,"date":"2024-05-30T10:43:15","date_gmt":"2024-05-30T14:43:15","guid":{"rendered":"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/?p=13348"},"modified":"2024-05-30T10:43:15","modified_gmt":"2024-05-30T14:43:15","slug":"population-genetics-dbsnp-alfa","status":"publish","type":"post","link":"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/2024\/05\/30\/population-genetics-dbsnp-alfa\/","title":{"rendered":"Explore Population Genetics in dbSNP with NCBI\u2019s Allele Frequency Aggregator (ALFA)"},"content":{"rendered":"<p><span data-contrast=\"auto\">Access to comprehensive and accurate allele frequency data is essential to understanding the impact of genetic variations on human health and disease. <\/span><a href=\"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/2020\/03\/26\/alfa\/?utm_source=ncbi_insights&amp;utm_medium=referral&amp;utm_campaign=alfa-dbsnp-20240530\"><span data-contrast=\"none\">Allele Frequency Aggregator (ALFA)<\/span><\/a><span data-contrast=\"auto\"> provides the <\/span><a href=\"https:\/\/www.ncbi.nlm.nih.gov\/snp?utm_source=ncbi_insights&amp;utm_medium=referral&amp;utm_campaign=alfa-dbsnp-20240530\"><span data-contrast=\"none\">Database of Single Nucleotide Polymorphisms (dbSNP)<\/span><\/a><span data-contrast=\"auto\"> with allele frequency data for 200K subjects from the <\/span><a href=\"https:\/\/www.ncbi.nlm.nih.gov\/gap\/?utm_source=ncbi_insights&amp;utm_medium=referral&amp;utm_campaign=alfa-dbsnp-20240530\"><span data-contrast=\"none\">Database of Genotypes and Phenotypes (dbGaP)<\/span><\/a><span data-contrast=\"auto\">. ALFA adheres to the <\/span><a href=\"https:\/\/www.go-fair.org\/fair-principles\/\"><span data-contrast=\"none\">Findable, Accessible, Interoperable, and Reusable (FAIR) Data Principles<\/span><\/a><span data-contrast=\"auto\"> providing open access to valuable allele frequency data.\u00a0<\/span><span data-ccp-props=\"{&quot;201341983&quot;:0,&quot;335559739&quot;:160,&quot;335559740&quot;:259}\">\u00a0<\/span><!--more--><\/p>\n<h5>Searching Allele Frequencies<\/h5>\n<p><span data-contrast=\"auto\">Search dbSNP for minor allele frequencies (MAF) within <\/span><a href=\"https:\/\/www.ncbi.nlm.nih.gov\/snp\/docs\/gsr\/data_inclusion\/?utm_source=ncbi_insights&amp;utm_medium=referral&amp;utm_campaign=alfa-dbsnp-20240530#population\"><span data-contrast=\"none\">ALFA\u2019s populations<\/span><\/a> <span data-contrast=\"auto\">to see genetic differences and get insights into human population history. This may also shed light on genetic variations and diseases that affect different populations and guide research on phenotype-genotype associations and possible treatments.\u00a0<\/span><span data-ccp-props=\"{&quot;201341983&quot;:0,&quot;335559739&quot;:160,&quot;335559740&quot;:259}\">\u00a0<\/span><\/p>\n<p><span data-contrast=\"auto\">Here are some <strong>examples<\/strong> that showcase the versatility and usefulness of ALFA searching in the SNP database.<\/span><span data-ccp-props=\"{&quot;201341983&quot;:0,&quot;335559739&quot;:160,&quot;335559740&quot;:259}\">\u00a0<\/span><\/p>\n<ul>\n<li><span style=\"font-size: 17px;\">A specific minor allele frequency or a range of MAFs in the ALFA populations:\u00a0<\/span><\/li>\n<\/ul>\n<div class=\"wptb-table-container wptb-table-13370\"><div class=\"wptb-table-container-matrix\" id=\"wptb-table-id-13370\" data-wptb-version=\"2.0.2\" data-wptb-pro-status=\"false\"><table class=\"wptb-preview-table wptb-element-main-table_setting-13370 edit-active\" data-reconstraction=\"1\" style=\"border: 1px solid rgb(209, 209, 209);\" data-wptb-table-tds-sum-max-width=\"131.60000000000002\" data-wptb-cells-width-auto-count=\"1\" data-wptb-horizontal-scroll-status=\"false\" data-wptb-extra-styles=\"LyogRW50ZXIgeW91ciBjdXN0b20gQ1NTIHJ1bGVzIGhlcmUgKi8=\" role=\"table\" data-table-columns=\"1\"><tbody><tr class=\"wptb-row\"><td class=\"wptb-cell\" data-y-index=\"0\" data-x-index=\"0\" style=\"border: 1px solid rgb(209, 209, 209);\" data-wptb-css-td-auto-width=\"true\"><div class=\"wptb-text-container wptb-ph-element wptb-element-text-597\" style=\"color: rgb(0, 0, 0); font-size: 15px;\"><div class=\"\" style=\"position: relative;\"><p><strong>Variants with MAF 0.01 in the European Population (ALFA_EUR]:<\/strong>&nbsp;<br>&nbsp;&nbsp;<a data-mce-href=\"https:\/\/www.ncbi.nlm.nih.gov\/snp\/?term=%2200000.0100%22%5BALFA_EUR%5D&amp;utm_source=ncbi_insights&amp;utm_medium=referral&amp;utm_campaign=alfa-dbsnp-20240530\" href=\"https:\/\/www.ncbi.nlm.nih.gov\/snp\/?term=%2200000.0100%22%5BALFA_EUR%5D&amp;utm_source=ncbi_insights&amp;utm_medium=referral&amp;utm_campaign=alfa-dbsnp-20240530\" style=\"color: rgb(74, 144, 226);\">&ldquo;00000.0100&rdquo;[ALFA_EUR]<\/a>&nbsp;<\/p><\/div><\/div><\/td><\/tr><tr class=\"wptb-row\"><td class=\"wptb-cell\" data-y-index=\"1\" data-x-index=\"0\" style=\"border: 1px solid rgb(209, 209, 209);\" data-wptb-css-td-auto-width=\"true\"><div class=\"wptb-text-container wptb-ph-element wptb-element-text-598\" style=\"color: rgb(0, 0, 0); font-size: 15px;\"><div class=\"\" style=\"position: relative;\"><p><strong>All common variants (MAF 0.01 to 0.5) in the African Populations [ALFA_AFR]:<\/strong> <a data-mce-href=\"https:\/\/www.ncbi.nlm.nih.gov\/snp\/?term=%2200000.0100%22%3A%2200000.5000%22%5BALFA_AFR%5D&amp;utm_source=ncbi_insights&amp;utm_medium=referral&amp;utm_campaign=alfa-dbsnp-20240530\" href=\"https:\/\/www.ncbi.nlm.nih.gov\/snp\/?term=%2200000.0100%22%3A%2200000.5000%22%5BALFA_AFR%5D&amp;utm_source=ncbi_insights&amp;utm_medium=referral&amp;utm_campaign=alfa-dbsnp-20240530\" style=\"color: rgb(74, 144, 226);\" data-mce-selected=\"inline-boundary\">&nbsp;\"00000.0100\":\"00000.5000\"[ALFA_AFR]<\/a><\/p><\/div><\/div><\/td><\/tr><\/tbody><\/table>\n<\/div><\/div>\n\n<ul>\n<li><span style=\"font-size: 17px;\">Minor allele frequencies or a frequency range of MAFs in Boolean searches with other dbSNP filters or search terms: <\/span><\/li>\n<\/ul>\n<div class=\"wptb-table-container wptb-table-13373\"><div class=\"wptb-table-container-matrix\" id=\"wptb-table-id-13373\" data-wptb-version=\"2.0.2\" data-wptb-pro-status=\"false\"><table class=\"wptb-preview-table wptb-element-main-table_setting-13373\" data-reconstraction=\"1\" style=\"border: 1px solid rgb(209, 209, 209); float: left;\" data-wptb-table-tds-sum-max-width=\"132\" data-wptb-cells-width-auto-count=\"1\" data-wptb-horizontal-scroll-status=\"false\" data-wptb-extra-styles=\"LyogRW50ZXIgeW91ciBjdXN0b20gQ1NTIHJ1bGVzIGhlcmUgKi8=\" role=\"table\" data-table-columns=\"1\" data-wptb-table-alignment=\"left\"><tbody><tr class=\"wptb-row\"><td class=\"wptb-cell\" data-y-index=\"0\" data-x-index=\"0\" style=\"border: 1px solid rgb(209, 209, 209);\" data-wptb-css-td-auto-width=\"true\"><div class=\"wptb-text-container wptb-ph-element wptb-element-text-597\" style=\"color: rgb(0, 0, 0); font-size: 15px;\"><div class=\"\" style=\"position: relative;\"><p><strong>Common variants in European populations [ALFA_EUR] that are rare in African populations [ALFA_AFR]: <\/strong><\/p><p><a data-mce-href=\"https:\/\/www.ncbi.nlm.nih.gov\/snp\/?term=%2200000.0100%22%3A%2200000.5000%22%5BALFA_EUR%5D+AND+%2200000.0010%22%3A%2200000.0110%22%5BALFA_AFR%5D&amp;utm_source=ncbi_insights&amp;utm_medium=referral&amp;utm_campaign=alfa-dbsnp-20240530\" href=\"https:\/\/www.ncbi.nlm.nih.gov\/snp\/?term=%2200000.0100%22%3A%2200000.5000%22%5BALFA_EUR%5D+AND+%2200000.0010%22%3A%2200000.0110%22%5BALFA_AFR%5D&amp;utm_source=ncbi_insights&amp;utm_medium=referral&amp;utm_campaign=alfa-dbsnp-20240530\">\"00000.0100\":\"00000.5000\"[ALFA_EUR] AND \"00000.0010\":\"00000.0110\"[ALFA_AFR]<\/a><\/p><\/div><\/div><\/td><\/tr><tr class=\"wptb-row\"><td class=\"wptb-cell\" data-y-index=\"1\" data-x-index=\"0\" style=\"border: 1px solid rgb(209, 209, 209);\" data-wptb-css-td-auto-width=\"true\"><div class=\"wptb-text-container wptb-ph-element wptb-element-text-598\" style=\"color: rgb(0, 0, 0); font-size: 15px;\"><div class=\"\" style=\"position: relative;\"><p><strong>Rare missense variants in the South Asian population [ALFA_SAS] that are identified as pathogenic alleles: <\/strong><\/p><p><a data-mce-href=\"https:\/\/www.ncbi.nlm.nih.gov\/snp\/?term=%2200000.0001%22%5BALFA_SAS%5D+%3A+%2200000.01000%22%5BALFA_SAS%5D+AND+%28pathogenic%5BClinical_Significance%5D+AND+missense+variant%5BFunction_Class%5D%29&amp;cmd=DetailsSearch&amp;utm_source=ncbi_insights&amp;utm_medium=referral&amp;utm_campaign=alfa-dbsnp-20240530\" href=\"https:\/\/www.ncbi.nlm.nih.gov\/snp\/?term=%2200000.0001%22%5BALFA_SAS%5D+%3A+%2200000.01000%22%5BALFA_SAS%5D+AND+%28pathogenic%5BClinical_Significance%5D+AND+missense+variant%5BFunction_Class%5D%29&amp;cmd=DetailsSearch&amp;utm_source=ncbi_insights&amp;utm_medium=referral&amp;utm_campaign=alfa-dbsnp-20240530\">\"00000.0001\"[ALFA_SAS] : \"00000.01000\"[ALFA_SAS] AND pathogenic[Clinical_Significance] AND missense variant[Function_Class]&nbsp;<\/a><\/p><\/div><\/div><\/td><\/tr><\/tbody><\/table><\/div><\/div>\n\n<p><img data-recalc-dims=\"1\" loading=\"lazy\" decoding=\"async\" data-attachment-id=\"13351\" data-permalink=\"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/2024\/05\/30\/population-genetics-dbsnp-alfa\/alfa-4\/\" data-orig-file=\"https:\/\/i0.wp.com\/ncbiinsights.ncbi.nlm.nih.gov\/wp-content\/uploads\/2024\/05\/ALFA.png?fit=938%2C1144&amp;ssl=1\" data-orig-size=\"938,1144\" data-comments-opened=\"1\" data-image-meta=\"{&quot;aperture&quot;:&quot;0&quot;,&quot;credit&quot;:&quot;&quot;,&quot;camera&quot;:&quot;&quot;,&quot;caption&quot;:&quot;&quot;,&quot;created_timestamp&quot;:&quot;0&quot;,&quot;copyright&quot;:&quot;&quot;,&quot;focal_length&quot;:&quot;0&quot;,&quot;iso&quot;:&quot;0&quot;,&quot;shutter_speed&quot;:&quot;0&quot;,&quot;title&quot;:&quot;&quot;,&quot;orientation&quot;:&quot;0&quot;}\" data-image-title=\"ALFA\" data-image-description=\"\" data-image-caption=\"\" data-medium-file=\"https:\/\/i0.wp.com\/ncbiinsights.ncbi.nlm.nih.gov\/wp-content\/uploads\/2024\/05\/ALFA.png?fit=246%2C300&amp;ssl=1\" data-large-file=\"https:\/\/i0.wp.com\/ncbiinsights.ncbi.nlm.nih.gov\/wp-content\/uploads\/2024\/05\/ALFA.png?fit=840%2C1024&amp;ssl=1\" class=\"alignright size-full wp-image-13351\" src=\"https:\/\/i0.wp.com\/ncbiinsights.ncbi.nlm.nih.gov\/wp-content\/uploads\/2024\/05\/ALFA.png?resize=938%2C1144&#038;ssl=1\" alt=\"Screenshot of dbSNP results and ALFA frequencies for a missense variant\" width=\"938\" height=\"1144\" srcset=\"https:\/\/i0.wp.com\/ncbiinsights.ncbi.nlm.nih.gov\/wp-content\/uploads\/2024\/05\/ALFA.png?w=938&amp;ssl=1 938w, https:\/\/i0.wp.com\/ncbiinsights.ncbi.nlm.nih.gov\/wp-content\/uploads\/2024\/05\/ALFA.png?resize=246%2C300&amp;ssl=1 246w, https:\/\/i0.wp.com\/ncbiinsights.ncbi.nlm.nih.gov\/wp-content\/uploads\/2024\/05\/ALFA.png?resize=840%2C1024&amp;ssl=1 840w, https:\/\/i0.wp.com\/ncbiinsights.ncbi.nlm.nih.gov\/wp-content\/uploads\/2024\/05\/ALFA.png?resize=123%2C150&amp;ssl=1 123w, https:\/\/i0.wp.com\/ncbiinsights.ncbi.nlm.nih.gov\/wp-content\/uploads\/2024\/05\/ALFA.png?resize=768%2C937&amp;ssl=1 768w, https:\/\/i0.wp.com\/ncbiinsights.ncbi.nlm.nih.gov\/wp-content\/uploads\/2024\/05\/ALFA.png?resize=221%2C270&amp;ssl=1 221w\" sizes=\"auto, (max-width: 938px) 100vw, 938px\" \/><span style=\"font-size: 17px;\"><i>Figure 1: dbSNP results and ALFA frequencies for a missense variant (<\/i><a style=\"background-color: #ffffff;\" href=\"https:\/\/www.ncbi.nlm.nih.gov\/snp\/rs17580?utm_source=ncbi_insights&amp;utm_medium=referral&amp;utm_campaign=alfa-dbsnp-20240530#frequency_tab\"><i>rs17580<\/i><\/a><i>) in the <a href=\"https:\/\/www.ncbi.nlm.nih.gov\/gene\/5265\/?utm_source=ncbi_insights&amp;utm_medium=referral&amp;utm_campaign=alfa-dbsnp-20240530\">SERPINA1 gene<\/a>. This is a globally common variant that can be associated with <\/i><a style=\"background-color: #ffffff;\" href=\"https:\/\/www.ncbi.nlm.nih.gov\/books\/NBK1519\/?utm_source=ncbi_insights&amp;utm_medium=referral&amp;utm_campaign=alfa-dbsnp-20240530#alpha1-a.Molecular_Genetics\"><i>alpha-1-antitrypsin deficiency<\/i><\/a><i>. It shows as a common variant in the ALFA European population but is much rarer in the African population<\/i>.\u00a0\u00a0<\/span><\/p>\n<h5 aria-level=\"2\">Advanced Search<\/h5>\n<p><span data-contrast=\"auto\">Use additional search terms and attributes such as gene name, other function classes (e.g., synonymous, frameshift, etc.), variant types, and others for more precise results. The SNP <\/span><a href=\"https:\/\/www.ncbi.nlm.nih.gov\/snp\/advanced?utm_source=ncbi_insights&amp;utm_medium=referral&amp;utm_campaign=alfa-dbsnp-20240530\"><span data-contrast=\"none\">Advanced Search Builder<\/span><\/a><span data-contrast=\"auto\"> can help with setting up complex Boolean queries.\u00a0<\/span><span data-ccp-props=\"{&quot;201341983&quot;:0,&quot;335559739&quot;:160,&quot;335559740&quot;:259}\">\u00a0<\/span><\/p>\n<h5 aria-level=\"2\">API Access<\/h5>\n<p><span data-contrast=\"auto\">You can use automated workflows through the E-Utilities API to search and retrieve ALFA data using automated workflows. Visit <\/span><a href=\"https:\/\/github.com\/ncbi\/dbsnp\/tree\/master\/tutorials\"><span data-contrast=\"none\">GitHub<\/span><\/a><span data-contrast=\"auto\"> for tutorials and demonstration code that show how to use the E-Utilities to access these data.<\/span><span data-ccp-props=\"{&quot;201341983&quot;:0,&quot;335559739&quot;:160,&quot;335559740&quot;:259}\">\u00a0<\/span><\/p>\n<h5 aria-level=\"5\">Stay up to date<\/h5>\n<p><span data-contrast=\"auto\">Follow us on social media\u202f<\/span><a href=\"https:\/\/twitter.com\/ncbi\"><span data-contrast=\"none\">@NCBI<\/span><\/a><span data-contrast=\"auto\">\u202fand\u202f<\/span><a href=\"https:\/\/public.govdelivery.com\/accounts\/USNLMOCPL\/subscriber\/new?topic_id=USNLMOCPL_52\"><span data-contrast=\"none\">join our mailing list<\/span><\/a><span data-contrast=\"auto\">\u202fto keep up to date with\u202fdbSNP\u202fand other NCBI news.<\/span><span data-ccp-props=\"{&quot;134233117&quot;:false,&quot;134233118&quot;:false,&quot;201341983&quot;:0,&quot;335557856&quot;:16777215,&quot;335559738&quot;:0,&quot;335559739&quot;:0,&quot;335559740&quot;:240}\">\u00a0<\/span><\/p>\n<h5 aria-level=\"2\">Questions?<\/h5>\n<p aria-level=\"2\"><span data-contrast=\"auto\">Please <\/span><a href=\"https:\/\/support.nlm.nih.gov\/support\/create-case\/\"><span data-contrast=\"none\">reach out to us<\/span><\/a><span data-contrast=\"auto\"> with questions or feedback.<\/span><span data-ccp-props=\"{&quot;134245418&quot;:true,&quot;134245529&quot;:true,&quot;201341983&quot;:0,&quot;335559738&quot;:0,&quot;335559739&quot;:0,&quot;335559740&quot;:240}\">\u00a0<\/span><span data-ccp-props=\"{&quot;201341983&quot;:0,&quot;335559739&quot;:160,&quot;335559740&quot;:259}\">\u00a0<\/span><\/p>\n","protected":false},"excerpt":{"rendered":"<p>Access to comprehensive and accurate allele frequency data is essential to understanding the impact of genetic variations on human health and disease. Allele Frequency Aggregator (ALFA) provides the Database of Single Nucleotide Polymorphisms (dbSNP) with allele frequency data for 200K subjects from the Database of Genotypes and Phenotypes (dbGaP). ALFA adheres to the Findable, Accessible, &hellip; <a href=\"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/2024\/05\/30\/population-genetics-dbsnp-alfa\/\" class=\"more-link\">Continue reading <span class=\"screen-reader-text\">Explore Population Genetics in dbSNP with NCBI\u2019s Allele Frequency Aggregator (ALFA)<\/span> <span class=\"meta-nav\">&rarr;<\/span><\/a><\/p>\n","protected":false},"author":42204617,"featured_media":13369,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"_coblocks_attr":"","_coblocks_dimensions":"","_coblocks_responsive_height":"","_coblocks_accordion_ie_support":"","jetpack_post_was_ever_published":false,"_jetpack_newsletter_access":"","_jetpack_dont_email_post_to_subs":false,"_jetpack_newsletter_tier_id":0,"_jetpack_memberships_contains_paywalled_content":false,"_jetpack_memberships_contains_paid_content":false,"footnotes":"","jetpack_publicize_message":"Explore Population Genetics in dbSNP with NCBI\u2019s Allele Frequency Aggregator (ALFA)","jetpack_publicize_feature_enabled":true,"jetpack_social_post_already_shared":true,"jetpack_social_options":{"image_generator_settings":{"template":"highway","enabled":false},"version":2}},"categories":[2248],"tags":[693060677,10192294],"table_tags":[],"class_list":["post-13348","post","type-post","status-publish","format-standard","has-post-thumbnail","hentry","category-whats-new","tag-dbgap-allele-frequency-aggregator-alfa","tag-dbsnp"],"jetpack_publicize_connections":[],"yoast_head":"<!-- This site is optimized with the Yoast SEO plugin v24.6 - https:\/\/yoast.com\/wordpress\/plugins\/seo\/ -->\n<title>Explore Population Genetics in dbSNP with NCBI\u2019s Allele Frequency Aggregator (ALFA) - NCBI Insights<\/title>\n<meta name=\"robots\" content=\"index, follow, max-snippet:-1, max-image-preview:large, max-video-preview:-1\" \/>\n<link rel=\"canonical\" href=\"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/2024\/05\/30\/population-genetics-dbsnp-alfa\/\" \/>\n<meta property=\"og:locale\" content=\"en_US\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"Explore Population Genetics in dbSNP with NCBI\u2019s Allele Frequency Aggregator (ALFA) - NCBI Insights\" \/>\n<meta property=\"og:description\" content=\"Access to comprehensive and accurate allele frequency data is essential to understanding the impact of genetic variations on human health and disease. Allele Frequency Aggregator (ALFA) provides the Database of Single Nucleotide Polymorphisms (dbSNP) with allele frequency data for 200K subjects from the Database of Genotypes and Phenotypes (dbGaP). 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