VariantProperties
Defined in file seqfeat.asn
C++ class: CVariantProperties
VariantProperties ::= SEQUENCE {
version INTEGER,
-- NOTE:
-- The format for most of these values is as an integer
-- Unless otherwise noted, these integers represent a bitwise OR (= simple
-- sum) of the possible values, and as such, these values represent the
-- specific bit flags that may be set for each of the possible attributes
-- here.
resource-link INTEGER {
preserved (1), -- Clinical, Pubmed, Cited, (0x01)
provisional (2), -- Provisional Third Party Annotations (0x02)
has3D (4), -- Has 3D strcture SNP3D table (0x04)
submitterLinkout (8), -- SNP->SubSNP->Batch link_out (0x08)
clinical (16), -- Clinical if LSDB, OMIM, TPA, Diagnostic (0x10)
genotypeKit (32) -- Marker exists on high density genotyping kit
-- (0x20)
} OPTIONAL,
gene-location INTEGER {
in-gene (1), -- Sequence intervals covered by a gene ID but not
-- having an aligned transcript (0x01)
near-gene-5 (2), -- Within 2kb of the 5' end of a gene feature
near-gene-3 (4), -- Within 0.5kb of the 3' end of a gene feature
intron (8), -- In Intron (0x08)
donor (16), -- In donor splice-site (0x10)
acceptor (32), -- In acceptor splice-site (0x20)
utr-5 (64), -- In 5' UTR (0x40)
utr-3 (128), -- In 3' UTR (0x80)
in-start-codon(256), -- the variant is observed in a start codon
-- (0x100)
in-stop-codon (512), -- the variant is observed in a stop codon
-- (0x200)
intergenic (1024), -- variant located between genes (0x400)
conserved-noncoding(2048) -- variant is located in a conserved
-- non-coding region (0x800)
} OPTIONAL,
effect INTEGER {
no-change (0), -- known to cause no functional changes
-- since 0 does not combine with any other bit
-- value, 'no-change' specifically implies that
-- there are no consequences
synonymous (1), -- one allele in the set does not change the encoded
-- amino acid (0x1)
nonsense (2), -- one allele in the set changes to STOP codon
-- (TER). (0x2)
missense (4), -- one allele in the set changes protein peptide
-- (0x4)
frameshift (8), -- one allele in the set changes all downstream
-- amino acids (0x8)
up-regulator (16), -- the variant causes increased transcription
-- (0x10)
down-regulator(32), -- the variant causes decreased transcription
-- (0x20)
methylation (64),
stop-gain (128), -- reference codon is not stop codon, but the snp
-- variant allele changes the codon to a
-- terminating codon.
stop-loss (256) -- reverse of STOP-GAIN: reference codon is a
-- stop codon, but a snp variant allele changes
-- the codon to a non-terminating codon.
} OPTIONAL,
mapping INTEGER {
has-other-snp (1), -- Another SNP has the same mapped positions
-- on reference assembly (0x01)
has-assembly-conflict (2), -- Weight 1 or 2 SNPs that map to different
-- chromosomes on different assemblies (0x02)
is-assembly-specific (4) -- Only maps to 1 assembly (0x04)
} OPTIONAL,
-- map-weight captures specificity of placement
-- NOTE: This is *NOT* a bitfield
map-weight INTEGER {
is-uniquely-placed(1),
placed-twice-on-same-chrom(2),
placed-twice-on-diff-chrom(3),
many-placements(10)
} OPTIONAL,
frequency-based-validation INTEGER {
is-mutation (1), -- low frequency variation that is cited in
-- journal or other reputable sources (0x01)
above-5pct-all (2), -- >5% minor allele freq in each and all
-- populations (0x02)
above-5pct-1plus (4), -- >5% minor allele freq in 1+ populations (0x04)
validated (8), -- Bit is set if the variant has a minor allele
-- observed in two or more separate chromosomes
above-1pct-all (16), -- >1% minor allele freq in each and all
-- populations (0x10)
above-1pct-1plus (32) -- >1% minor allele freq in 1+ populations (0x20)
} OPTIONAL,
genotype INTEGER {
in-haplotype-set (1), -- Exists in a haplotype tagging set (0x01)
has-genotypes (2) -- SNP has individual genotype (0x02)
} OPTIONAL,
-- project IDs are IDs from BioProjects
-- in order to report information about project relationships, we
-- require projects to be registered
-- This field in many ways duplicates dbxrefs; however, the
-- intention of this field is to more adequately reflect
-- ownership and data source
--
-- 11/9/2010: DO NOT USE
-- This field was changed in the spec in a breaking way; using it will
-- break clients. We are officially suppressing / abandoning this field.
-- Clients who need to use this should instead place the data in
-- Seq-feat.dbxref, using the db name 'BioProject'
project-data SET OF INTEGER OPTIONAL,
quality-check INTEGER {
contig-allele-missing (1), -- Reference sequence allele at the mapped
-- position is not present in the SNP
-- allele list, adjusted for orientation
-- (0x01)
withdrawn-by-submitter (2), -- One member SS is withdrawn by submitter
-- (0x02)
non-overlapping-alleles (4), -- RS set has 2+ alleles from different
-- submissions and these sets share no
-- alleles in common (0x04)
strain-specific (8), -- Straing specific fixed difference (0x08)
genotype-conflict (16) -- Has Genotype Conflict (0x10)
} OPTIONAL,
confidence INTEGER {
unknown (0),
likely-artifact (1),
other (255)
} OPTIONAL,
-- has this variant been validated?
-- While a boolean flag offers no subtle distinctions of validation
-- methods, occasionally it is only known as a single boolean value
-- NOTE: this flag is redundant and should be omitted if more comprehensive
-- validation information is present
other-validation BOOLEAN OPTIONAL,
-- origin of this allele, if known
-- note that these are powers-of-two, and represent bits; thus, we can
-- represent more than one state simultaneously through a bitwise OR
allele-origin INTEGER {
unknown (0),
germline (1),
somatic (2),
inherited (4),
paternal (8),
maternal (16),
de-novo (32),
biparental (64),
uniparental (128),
not-tested (256),
tested-inconclusive (512),
not-reported (1024),
-- stopper - 2^31
other (1073741824)
} OPTIONAL,
-- observed allele state, if known
-- NOTE: THIS IS NOT A BITFIELD!
allele-state INTEGER {
unknown (0),
homozygous (1),
heterozygous (2),
hemizygous (3),
nullizygous (4),
other (255)
} OPTIONAL,
-- NOTE:
-- 'allele-frequency' here refers to the minor allele frequency of the
-- default population
allele-frequency REAL OPTIONAL,
-- is this variant the ancestral allele?
is-ancestral-allele BOOLEAN OPTIONAL
}