Genomic Variant

A genetic variant identified in genomic sequencing data as processed by Regeneron Genetics Center pipelines

PharmaceuticalsBiotechnologyGenomicsBioinformaticsDrug DiscoveryClinical ResearchLife SciencesFortune 500

Properties

Name	Type	Description
variantId	string	Unique variant identifier (e.g., rsID or internal ID)
chromosome	string	Chromosome designation (1-22, X, Y, MT)
position	integer	Genomic position on the chromosome (1-based)
referenceAllele	string	Reference genome allele
alternateAllele	string	Alternate (non-reference) allele
variantType	string	Classification of the genetic variant
gene	string	Gene symbol in which the variant is located
hgvs	string	HGVS nomenclature representation of the variant
clinicalSignificance	string	ClinVar clinical significance classification
alleleFrequency	number	Population allele frequency (0 to 1)
qualityScore	number	Variant calling quality score
depth	integer	Read depth at the variant position
genotype	string	Sample genotype (e.g., 0/1 for heterozygous, 1/1 for homozygous alternate)
phenotypes	array	Associated phenotype or disease terms (HPO or OMIM)

View JSON Schema on GitHub

JSON Schema

{
  "$schema": "https://json-schema.org/draft/2020-12/schema",
  "$id": "https://api-evangelist.github.io/regeneron-pharmaceuticals/json-schema/regeneron-genomic-variant-schema.json",
  "title": "Genomic Variant",
  "description": "A genetic variant identified in genomic sequencing data as processed by Regeneron Genetics Center pipelines",
  "type": "object",
  "required": ["variantId", "chromosome", "position", "referenceAllele", "alternateAllele"],
  "properties": {
    "variantId": {
      "type": "string",
      "description": "Unique variant identifier (e.g., rsID or internal ID)"
    },
    "chromosome": {
      "type": "string",
      "description": "Chromosome designation (1-22, X, Y, MT)"
    },
    "position": {
      "type": "integer",
      "minimum": 1,
      "description": "Genomic position on the chromosome (1-based)"
    },
    "referenceAllele": {
      "type": "string",
      "pattern": "^[ACGT]+$",
      "description": "Reference genome allele"
    },
    "alternateAllele": {
      "type": "string",
      "pattern": "^[ACGT]+$",
      "description": "Alternate (non-reference) allele"
    },
    "variantType": {
      "type": "string",
      "enum": ["SNP", "INDEL", "CNV", "SV", "INSERTION", "DELETION"],
      "description": "Classification of the genetic variant"
    },
    "gene": {
      "type": "string",
      "description": "Gene symbol in which the variant is located"
    },
    "hgvs": {
      "type": "string",
      "description": "HGVS nomenclature representation of the variant"
    },
    "clinicalSignificance": {
      "type": "string",
      "enum": ["Pathogenic", "Likely Pathogenic", "Uncertain Significance", "Likely Benign", "Benign"],
      "description": "ClinVar clinical significance classification"
    },
    "alleleFrequency": {
      "type": "number",
      "minimum": 0,
      "maximum": 1,
      "description": "Population allele frequency (0 to 1)"
    },
    "qualityScore": {
      "type": "number",
      "description": "Variant calling quality score"
    },
    "depth": {
      "type": "integer",
      "minimum": 0,
      "description": "Read depth at the variant position"
    },
    "genotype": {
      "type": "string",
      "description": "Sample genotype (e.g., 0/1 for heterozygous, 1/1 for homozygous alternate)"
    },
    "phenotypes": {
      "type": "array",
      "items": { "type": "string" },
      "description": "Associated phenotype or disease terms (HPO or OMIM)"
    }
  },
  "additionalProperties": false
}