The default version of our dbSNP annotation is currently referring to dbSNP143 (using hg38 coordinates) as shown below. However, users can also retrieve older versions of dbSNP: dbSNP141, dbSNP138, dbSNP137, dbSNP135, dbSNP132, dbSNP131, dbSNP130, dbSNP129. The 129 and 130 versions use hg18 as a reference genome, 131, 132, 135, 137, 138 and 141 use hg19 and 143 uses hg38. The archived versions can be used by a variant tools project by referring to their specific names - for example: dbSNP-hg18_129.
dbSNP143 has many more flags and fields than previous versions. It also does not contain all variants that are defined in dbSNP141 and earlier.
A dbSNP entry might match multiple variants. For example, rs111688037 matches variants T->A and T->C at chr6:31602679.
% vtools show annotation dbSNP -v1
Annotation database dbSNP (version hg38_143)
Description: dbSNP version 143, created using vcf file downloaded from NCBI
Database type: variant
Reference genome hg38: chr, pos, ref, alt
chr (char)
pos (int)
name (char) DB SNP ID (rsname)
ref (char) Reference allele (as on the + strand)
alt (char) Alternative allele (as on the + strand)
FILTER (char) Inconsistent Genotype Submission For At Least One Sample
RS (int) dbSNP ID (i.e. rs number)
RSPOS (int) Chr position reported in dbSNP
RV (int) RS orientation is reversed
VP (char) Variation Property. Documentation
is at ftp://ftp.ncbi.nlm.nih.gov/snp/specs/dbSNP_BitField_latest.pdf
GENEINFO (char) Pairs each of gene symbol:gene id.
The gene symbol and id are delimited by a colon (</summary>
and each pair is delimited by a vertical bar (|)
dbSNPBuildID (int) First dbSNP Build for RS
SAO (int) Variant Allele Origin: 0 - unspecified, 1 - Germline, 2 - Somatic,
3 - Both
SSR (int) Variant Suspect Reason Codes (may be more than one value
added together)
0 - unspecified, 1 - Paralog, 2 - byEST, 4 - oldAlign, 8 - Para_EST,
16 - 1kg_failed, 1024 - other
WGT (int) Weight, 00 - unmapped, 1 - weight 1, 2 - weight 2, 3 - weight 3 or
more
VC (char) Variation Class
PM_flag (int) Variant is Precious(Clinical,Pubmed Cited)
TPA_flag (int) Provisional Third Party Annotation(TPA)
(currently rs from PHARMGKB who will give phenotype data)
PMC_flag (int) Links exist to PubMed Central article
S3D_flag (int) Has 3D structure - SNP3D table
SLO_flag (int) Has SubmitterLinkOut - From SNP->SubSNP->Batch.link_out
NSF_flag (int) Has non-synonymous frameshift A coding region variation where one
allele in the set changes all downstream amino acids.
FxnClass = 44
NSM_flag (int) Has non-synonymous missense A coding region variation where one
allele in the set changes protein peptide. FxnClass = 42
NSN_flag (int) Has non-synonymous nonsense A coding region variation where one
allele in the set changes to STOP codon (TER). FxnClass = 41
REF_flag_flag (int) Has reference A coding region variation where one allele in the
set is identical to the reference sequence. FxnCode = 8
SYN_flag (int) Has synonymous A coding region variation where one allele in the
set does not change the encoded amino acid. FxnCode = 3
U3_flag (int) In 3' UTR Location is in an untranslated region (UTR).
FxnCode = 53
U5_flag (int) In 5' UTR Location is in an untranslated region (UTR).
FxnCode = 55
ASS_flag (int) In acceptor splice site FxnCode = 73
DSS_flag (int) In donor splice-site FxnCode = 75
INT_flag (int) In Intron FxnCode = 6
R3_flag (int) In 3' gene region FxnCode = 13
R5_flag (int) In 5' gene region FxnCode = 15
OTH_flag (int) Has other variant with exactly the same set of mapped positions on
NCBI refernce assembly.
CFL_flag (int) Has Assembly conflict. This is for weight 1 and 2 variant that maps to
different chromosomes on different assemblies.
ASP_flag (int) Is Assembly specific. This is set if the variant only maps to one
assembly
MUT_flag (int) Is mutation (journal citation, explicit fact): a low frequency
variation that is cited in journal and other reputable sources
VLD_flag (int) Is Validated. This bit is set if the variant has 2+ minor
allele count based on frequency or genotype data.
G5A_flag (int) >5% minor allele frequency in each and all populations
G5_flag (int) >5% minor allele frequency in 1+ populations
HD_flag (int) Marker is on high density genotyping kit (50K density or greater).
The variant may have phenotype associations present in dbGaP.
GNO_flag (int) Genotypes available. The variant has individual genotype
(in SubInd table).
KGValidated_flag (int)
1000 Genome validated
KGPhase1_flag (int) 1000 Genome phase 1 (incl. June Interim phase 1)
KGPilot123_flag (int) 1000 Genome discovery all pilots 2010(1,2,3)
KGPROD_flag (int) Has 1000 Genome submission
OTHERKG_flag (int) non-1000 Genome submission
PH3_flag (int) HAP_MAP Phase 3 genotyped: filtered, non-redundant
CDA_flag (int) Variation is interrogated in a clinical diagnostic assay
LSD_flag (int) Submitted from a locus-specific database
MTP_flag (int) Microattribution/third-party annotation(TPA:GWAS,PAGE)
OM_flag (int) Has OMIM/OMIA
NOC_flag (int) Contig allele not present in variant allele list.
The reference sequence allele at the mapped position is not
present in the variant allele list, adjusted for orientation.
WTD_flag (int) Is Withdrawn by submitter If one member ss is withdrawn by submitter,
then this bit is set. If all member ss' are withdrawn,
then the rs is deleted to SNPHistory
NOV_flag (int) Rs cluster has non-overlapping allele sets.
True when rs set has more than 2 alleles from different submissions
and these sets share no alleles in common.
CAF (char) An ordered, comma delimited list of allele frequencies based on
1000Genomes, starting with the reference allele
followed by alternate alleles as ordered in the ALT column.
Where a 1000Genomes alternate allele is not in the dbSNPs alternate
allele set, the allele is added to the ALT column.
The minor allele is the second largest value in the list, and
was previuosly reported in VCF as the GMAF.
This is the GMAF reported on the RefSNP and EntrezSNP pages
and VariationReporter
COMMON (int) RS is a common SNP. A common SNP is one that has at least one
1000Genomes population with a minor allele of frequency >= 1%
and for which 2 or more founders contribute to that
minor allele frequency.
% vtools show annotation dbSNP-hg19_141 -v2
Annotation database dbSNP (version hg19_141)
Description: dbSNP version 141
Database type: variant
Number of records: 58,691,269
Distinct variants: 57,577,990
Reference genome hg19: chr, start, refNCBI, alt
Field: chr
Type: string
Missing entries: 0
Unique Entries: 25
Field: start
Type: integer
Comment: start position in chrom (1-based)
Missing entries: 0
Unique Entries: 48,758,859
Range: 56 - 249240605
Field: end
Type: integer
Comment: end position in chrom (1-based). start=end means zero-length feature
Missing entries: 0
Unique Entries: 48,957,633
Range: 56 - 249240605
Field: name
Type: string
Comment: dbSNP reference SNP identifier
Missing entries: 0
Unique Entries: 58,096,504
Field: strand
Type: string
Comment: which DNA strand contains the observed alleles
Missing entries: 0
Unique Entries: 2
Field: refNCBI
Type: string
Comment: Reference genomic sequence from dbSNP
Missing entries: 0
Unique Entries: 164,868
Field: refUCSC
Type: string
Comment: Reference genomic sequence from UCSC lookup of chrom,chromStart,
chromEnd
Missing entries: 0
Unique Entries: 187,096
Field: observed
Type: string
Comment: Strand-specific observed alleles
Missing entries: 0
Unique Entries: 205,862
Field: alt
Type: string
Comment: alternate allele on the '+' strand
Missing entries: 0
Unique Entries: 30,716
Field: molType
Type: string
Comment: sample type, can be one of unknown, genomic or cDNA
Missing entries: 0
Unique Entries: 3
Field: class
Type: string
Comment: Class of variant (single, in-del, het, named, mixed,
insertion, deletion etc
Missing entries: 0
Unique Entries: 6
Field: valid
Type: string
Comment: validation status, can be unknown, by-cluster, by-frequency,
by-submitter, by-2hit-2allele, by-hapmap, and by-1000genomes
Missing entries: 0
Unique Entries: 63
Field: avHet
Type: float
Comment: Average heterozygosity from all observations
Missing entries: 0
Unique Entries: 39,766
Range: 0 - 0.999999
Field: avHetSE
Type: float
Comment: Standard error for the average heterozygosity
Missing entries: 0
Unique Entries: 46,007
Range: 0 - 0.305748
Field: func
Type: string
Comment: Functional cetegory of the SNP (coding-synon, coding-nonsynon,
intron, etc.)
Missing entries: 0
Unique Entries: 648
Field: locType
Type: string
Comment: Type of mapping inferred from size on reference.
Missing entries: 0
Unique Entries: 6