New SNP Attributes
New attributes have been added to dbSNP to allow searching and filtering of human variation by the following characteristics.
Please contact snp-admin@ncbi.nlm.nih.gov if you have any questions or comments.
Attribute
RS Count (Build 132)
Allele Origin:The rs report summarizes the reported origin(s) of the variant allele asserted by each submitter for the submitted SNP (ss) . Current values are germline, somatic, and unknown. Additional attributes will be added in the future release to include:
- not-tested
- tested-inconclusive
- other
423
Clinical significance:The significance of the indicated allele.
The supported values are:
- unknown
- untested
- non-pathogenic
- probable-non-pathogenic
- probable-pathogenic
- pathogenic
- drug-response
- histocompatibility
- other
13105
Global minor allele frequency (MAF):dbSNP is reporting the minor allele frequency for each rs included in a default global population. Since this is being provided to distinguish common polymorphism from rare variants, the MAF is actually the second most frequent allele value. In other words, if there are 3 alleles, with frequencies of 0.50, 0.49, and 0.01, the MAF will be reported as 0.49. The current default global population is 1000Genome phase 1 genotype data from 629 worldwide individuals, released in the 08-04-2010 dataset.
14946243
Suspect:Variation suspected to be false positive due to artifacts of the presence of a paralogous sequence in the genome (Musumeci et al. 2010) (Sudmant et al. 2010) or evidence suggested sequencing error or computation artifacts.
105630
Below are examples of the attributes shown on web pages and schema changes.
A. Allele Origin
Indicated as Germline or Somatic for each allele
B. Clinical Significance
Click on "VarView" or "OMIM" to view phenotype
C. Global MAF
The minor allele (G), frequency (0.003), and allele count (3) is shown
D. Suspected
A red "?" icon is shown for suspected SNP in the "Validation" row
A. Allele Origin
Indicated as Germline or Somatic for each allele
B. Clinical Significance
Click on icon under "Clinical Source" to view effect in Variation Viewer
C. Global MAF
MAF is shown for the corresponding allele
D. Suspected
A red "?" icon is shown for suspected SNP under the "Validation" column
A. Allele Origin
Indicated as Germline or Somatic for the variation under "Origin" column
B. Clinical Significance
shown under "Clinical Intrepretation" column
C. Global MAF
frequency is shown under minor allele frequency (MAF) column
D. Suspected
A red "?" icon is shown for suspected SNP under the "Suspect" column
SNP Attribute
XML Element
Entrez Search and Eutils Retrieval
The SNP attributes can be search from the web using the field and terms below or selected from the limit page. The search can also be performed programatically using eUtils eSearch. Note: eUtils eFetch is currently being updated to support retrieval of variations with the new attributes. We'll let you know when the update is done.
SNP Attribute
Search Field (type)
Search Terms
A. Allele Origin
ALLELE_ORIGIN (text)
somatic
D. Suspected
SUSPECTED (text)
paralog
SNP Attribute
VCF Tag
A. Allele Origin
##INFO=<ID=SAO,Number=1,Type=Integer,Description="SNP Allele Origin: 0 - unspecified, 1 - Germline, 2 - Somatic, 3 - Both">
B. Clinical Significance
##INFO=<ID=SCS,Number=1,Type=Integer,Description="SNP Clinical Significance, 0 - unknown, 1 - untested, 2 - non-pathogenic, 3 - probable-non-pathogenic, 4 - probable-pathogenic, 5 - pathogenic, 6 - drug-response, 7 - histocompatibility, 255 - other">
C. Global MAF
##INFO=<ID=GMAF,Number=1,Type=Float,Description="Global Minor Allele Frequency [0, 0.5]; global population is 1000GenomesProject phase 1 genotype data from 629 individuals, released in the 08-04-2010 dataset">
D. Suspected
##INFO=<ID=SSR,Number=1,Type=Integer,Description="SNP Suspect Reason Code, 0 - unspecified, 1 - Paralog, 2 - byEST, 3 - Para_EST, 4 - oldAlign, 5 - other">