Variation Data Models

---

Two different data models are managed:

• Variation
• Variation Phenotype Annotation

---

Variation

{
	"_id" : ObjectId("536a5d933381301574b36f9c"),
	"id" : "rs14171",
	"chromosome" : "1",
	"start" : 21544177,
	"end" : 21544177,
	"strand" : "1",
	"type" : "SNV",
	"reference" : "G",
	"alternate" : "A",
	"alleleString" : "G/A",
	"ancestralAllele" : "G",
	"displayConsequenceType" : "3_prime_UTR_variant",
	"consequenceTypes" : [
		"3_prime_UTR_variant",
		"downstream_gene_variant"
	],
	"transcriptVariations" : [
		{
			"transcriptId" : "ENST00000415912",
			"alleleString" : "G/A",
			"somatic" : "0",
			"consequenceTypes" : [
				"3_prime_UTR_variant"
			],
			"cdsStart" : 0,
			"cdsEnd" : 0,
			"cdnaStart" : 4662,
			"cdnaEnd" : 4662,
			"translationStart" : 0,
			"translationEnd" : 0,
			"distanceToTranscript" : 437,
			"codonAlleleString" : "",
			"peptideAlleleString" : "",
			"hgvsGenomic" : "1:g.21544177G>A",
			"hgvsTranscript" : "ENST00000415912.2:c.*2271C>T",
			"hgvsProtein" : "",
			"polyphenPrediction" : "",
			"polyphenScore" : 0,
			"siftPrediction" : "",
			"siftScore" : 0
		},
		{
			"transcriptId" : "ENST00000357071",
			"alleleString" : "G/A",
			"somatic" : "0",
			"consequenceTypes" : [
				"downstream_gene_variant"
			],
			"cdsStart" : 0,
			"cdsEnd" : 0,
			"cdnaStart" : 0,
			"cdnaEnd" : 0,
			"translationStart" : 0,
			"translationEnd" : 0,
			"distanceToTranscript" : 900,
			"codonAlleleString" : "",
			"peptideAlleleString" : "",
			"hgvsGenomic" : "1:g.21544177G>A",
			"hgvsTranscript" : "",
			"hgvsProtein" : "",
			"polyphenPrediction" : "",
			"polyphenScore" : 0,
			"siftPrediction" : "",
			"siftScore" : 0
		},
		{
			"transcriptId" : "ENST00000531334",
			"alleleString" : "G/A",
			"somatic" : "0",
			"consequenceTypes" : [
				"downstream_gene_variant"
			],
			"cdsStart" : 0,
			"cdsEnd" : 0,
			"cdnaStart" : 0,
			"cdnaEnd" : 0,
			"translationStart" : 0,
			"translationEnd" : 0,
			"distanceToTranscript" : 2130,
			"codonAlleleString" : "",
			"peptideAlleleString" : "",
			"hgvsGenomic" : "1:g.21544177G>A",
			"hgvsTranscript" : "",
			"hgvsProtein" : "",
			"polyphenPrediction" : "",
			"polyphenScore" : 0,
			"siftPrediction" : "",
			"siftScore" : 0
		},
		{
			"transcriptId" : "ENST00000374893",
			"alleleString" : "G/A",
			"somatic" : "0",
			"consequenceTypes" : [
				"downstream_gene_variant"
			],
			"cdsStart" : 0,
			"cdsEnd" : 0,
			"cdnaStart" : 0,
			"cdnaEnd" : 0,
			"translationStart" : 0,
			"translationEnd" : 0,
			"distanceToTranscript" : 2175,
			"codonAlleleString" : "",
			"peptideAlleleString" : "",
			"hgvsGenomic" : "1:g.21544177G>A",
			"hgvsTranscript" : "",
			"hgvsProtein" : "",
			"polyphenPrediction" : "",
			"polyphenScore" : 0,
			"siftPrediction" : "",
			"siftScore" : 0
		},
		{
			"transcriptId" : "ENST00000436918",
			"alleleString" : "G/A",
			"somatic" : "0",
			"consequenceTypes" : [
				"downstream_gene_variant"
			],
			"cdsStart" : 0,
			"cdsEnd" : 0,
			"cdnaStart" : 0,
			"cdnaEnd" : 0,
			"translationStart" : 0,
			"translationEnd" : 0,
			"distanceToTranscript" : 2210,
			"codonAlleleString" : "",
			"peptideAlleleString" : "",
			"hgvsGenomic" : "1:g.21544177G>A",
			"hgvsTranscript" : "",
			"hgvsProtein" : "",
			"polyphenPrediction" : "",
			"polyphenScore" : 0,
			"siftPrediction" : "",
			"siftScore" : 0
		},
		{
			"transcriptId" : "ENST00000264205",
			"alleleString" : "G/A",
			"somatic" : "0",
			"consequenceTypes" : [
				"downstream_gene_variant"
			],
			"cdsStart" : 0,
			"cdsEnd" : 0,
			"cdnaStart" : 0,
			"cdnaEnd" : 0,
			"translationStart" : 0,
			"translationEnd" : 0,
			"distanceToTranscript" : 2253,
			"codonAlleleString" : "",
			"peptideAlleleString" : "",
			"hgvsGenomic" : "1:g.21544177G>A",
			"hgvsTranscript" : "",
			"hgvsProtein" : "",
			"polyphenPrediction" : "",
			"polyphenScore" : 0,
			"siftPrediction" : "",
			"siftScore" : 0
		}
	],
	"xrefs" : [ ],
	"minorAllele" : "",
	"minorAlleleFreq" : "",
	"validationStatus" : "",
	"evidence" : "Multiple_observations",
	"chunkIds" : [
		"1_21544_1k"
	]
}

Variation phenotype annotation

{
	"_id" : ObjectId("536a55713381301574550620"),
	"id" : "rs10283629",
	"chromosome" : "9",
	"start" : 21157695,
	"end" : 21157695,
	"strand" : "1",
	"phenotype" : "High Density Lipoprotein Cholesterol",
	"source" : "Teslovich",
	"clinicalSignificance" : "",
	"associatedGenes" : [ ],
	"riskAllele" : "A",
	"pValue" : 0.6806,
	"oddsRatio" : -1,
	"inheritanceType" : "",
	"externalId" : "",
	"chunkIds" : [
		"9_21157_1k"
	]
}