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GeneBe API Showcase

This page demonstrates how to use the GeneBe API to query variant information. The API provides programmatic access to genomic annotations and variant data.

API presented here should be used for checking single variants. If you want to check many variants at once, please use other API endpoints that you will find in the documentation.

Documentation & Advanced Usage

Complete API documentation:docs.genebe.net/docs/api/overview/

Interactive endpoint tester:api.genebe.net/cloud/gb-api-doc/swagger-ui/

Python client for pandas:pypi.org/project/genebe/

Java CLI for VCF files:github.com/pstawinski/genebe-cli

All tools documented at:docs.genebe.net

API Request Examples for Variant: 10-96551294-C-CAGCAAATATCTGACATCCAGAACA (hg38)

Bash / cURL Example

bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=10&pos=96551294&ref=C&alt=CAGCAAATATCTGACATCCAGAACA&genome=hg38&allGenes=true"

API Response

json
{
  "variants": [
    {
      "chr": "10",
      "pos": 96551294,
      "ref": "C",
      "alt": "CAGCAAATATCTGACATCCAGAACA",
      "effect": "conservative_inframe_insertion",
      "transcript": "ENST00000371142.9",
      "consequences": [
        {
          "aa_ref": "A",
          "aa_alt": "ACSGCQIFA",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "conservative_inframe_insertion"
          ],
          "exon_rank": 7,
          "exon_rank_end": null,
          "exon_count": 15,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "TM9SF3",
          "gene_hgnc_id": 21529,
          "hgvs_c": "c.909_910insTGTTCTGGATGTCAGATATTTGCT",
          "hgvs_p": "p.Ala303_Val304insCysSerGlyCysGlnIlePheAla",
          "transcript": "NM_020123.4",
          "protein_id": "NP_064508.3",
          "transcript_support_level": null,
          "aa_start": 303,
          "aa_end": null,
          "aa_length": 589,
          "cds_start": 909,
          "cds_end": null,
          "cds_length": 1770,
          "cdna_start": 1086,
          "cdna_end": null,
          "cdna_length": 6100,
          "mane_select": "ENST00000371142.9",
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "A",
          "aa_alt": "ACSGCQIFA",
          "canonical": true,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "conservative_inframe_insertion"
          ],
          "exon_rank": 7,
          "exon_rank_end": null,
          "exon_count": 15,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "TM9SF3",
          "gene_hgnc_id": 21529,
          "hgvs_c": "c.909_910insTGTTCTGGATGTCAGATATTTGCT",
          "hgvs_p": "p.Ala303_Val304insCysSerGlyCysGlnIlePheAla",
          "transcript": "ENST00000371142.9",
          "protein_id": "ENSP00000360184.4",
          "transcript_support_level": 1,
          "aa_start": 303,
          "aa_end": null,
          "aa_length": 589,
          "cds_start": 909,
          "cds_end": null,
          "cds_length": 1770,
          "cdna_start": 1086,
          "cdna_end": null,
          "cdna_length": 6100,
          "mane_select": "NM_020123.4",
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "A",
          "aa_alt": "ACSGCQIFA",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "conservative_inframe_insertion"
          ],
          "exon_rank": 7,
          "exon_rank_end": null,
          "exon_count": 15,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "TM9SF3",
          "gene_hgnc_id": 21529,
          "hgvs_c": "c.963_964insTGTTCTGGATGTCAGATATTTGCT",
          "hgvs_p": "p.Ala321_Val322insCysSerGlyCysGlnIlePheAla",
          "transcript": "XM_011539976.3",
          "protein_id": "XP_011538278.1",
          "transcript_support_level": null,
          "aa_start": 321,
          "aa_end": null,
          "aa_length": 607,
          "cds_start": 963,
          "cds_end": null,
          "cds_length": 1824,
          "cdna_start": 1361,
          "cdna_end": null,
          "cdna_length": 6375,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": false,
          "protein_coding": false,
          "strand": false,
          "consequences": [
            "non_coding_transcript_exon_variant"
          ],
          "exon_rank": 2,
          "exon_rank_end": null,
          "exon_count": 4,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "TM9SF3",
          "gene_hgnc_id": 21529,
          "hgvs_c": "n.133_134insTGTTCTGGATGTCAGATATTTGCT",
          "hgvs_p": null,
          "transcript": "ENST00000490192.1",
          "protein_id": null,
          "transcript_support_level": 4,
          "aa_start": null,
          "aa_end": null,
          "aa_length": null,
          "cds_start": -4,
          "cds_end": null,
          "cds_length": null,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": 884,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": false,
          "protein_coding": false,
          "strand": false,
          "consequences": [
            "non_coding_transcript_exon_variant"
          ],
          "exon_rank": 7,
          "exon_rank_end": null,
          "exon_count": 15,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "TM9SF3",
          "gene_hgnc_id": 21529,
          "hgvs_c": "n.1247_1248insTGTTCTGGATGTCAGATATTTGCT",
          "hgvs_p": null,
          "transcript": "ENST00000649367.1",
          "protein_id": null,
          "transcript_support_level": null,
          "aa_start": null,
          "aa_end": null,
          "aa_length": null,
          "cds_start": -4,
          "cds_end": null,
          "cds_length": null,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": 6250,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "downstream_gene_variant"
          ],
          "exon_rank": null,
          "exon_rank_end": null,
          "exon_count": 7,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "TM9SF3",
          "gene_hgnc_id": 21529,
          "hgvs_c": "c.*16_*17insTGTTCTGGATGTCAGATATTTGCT",
          "hgvs_p": null,
          "transcript": "ENST00000443638.1",
          "protein_id": "ENSP00000401152.1",
          "transcript_support_level": 3,
          "aa_start": null,
          "aa_end": null,
          "aa_length": 252,
          "cds_start": -4,
          "cds_end": null,
          "cds_length": 761,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": 868,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        }
      ],
      "gene_symbol": "TM9SF3",
      "gene_hgnc_id": 21529,
      "dbsnp": "rs2134143642",
      "frequency_reference_population": null,
      "hom_count_reference_population": 0,
      "allele_count_reference_population": 0,
      "gnomad_exomes_af": null,
      "gnomad_genomes_af": null,
      "gnomad_exomes_ac": null,
      "gnomad_genomes_ac": null,
      "gnomad_exomes_homalt": null,
      "gnomad_genomes_homalt": null,
      "gnomad_mito_homoplasmic": null,
      "gnomad_mito_heteroplasmic": null,
      "computational_score_selected": null,
      "computational_prediction_selected": null,
      "computational_source_selected": null,
      "splice_score_selected": null,
      "splice_prediction_selected": null,
      "splice_source_selected": null,
      "revel_score": null,
      "revel_prediction": null,
      "alphamissense_score": null,
      "alphamissense_prediction": null,
      "bayesdelnoaf_score": null,
      "bayesdelnoaf_prediction": null,
      "phylop100way_score": 0.022,
      "phylop100way_prediction": "Benign",
      "spliceai_max_score": null,
      "spliceai_max_prediction": null,
      "dbscsnv_ada_score": null,
      "dbscsnv_ada_prediction": null,
      "apogee2_score": null,
      "apogee2_prediction": null,
      "mitotip_score": null,
      "mitotip_prediction": null,
      "acmg_score": 2,
      "acmg_classification": "Uncertain_significance",
      "acmg_criteria": "PM4",
      "acmg_by_gene": [
        {
          "score": 2,
          "benign_score": 0,
          "pathogenic_score": 2,
          "criteria": [
            "PM4"
          ],
          "verdict": "Uncertain_significance",
          "transcript": "ENST00000371142.9",
          "gene_symbol": "TM9SF3",
          "hgnc_id": 21529,
          "effects": [
            "conservative_inframe_insertion"
          ],
          "inheritance_mode": "AD",
          "hgvs_c": "c.909_910insTGTTCTGGATGTCAGATATTTGCT",
          "hgvs_p": "p.Ala303_Val304insCysSerGlyCysGlnIlePheAla"
        }
      ],
      "clinvar_disease": "not provided",
      "clinvar_classification": "Uncertain significance",
      "clinvar_review_status": "no assertion criteria provided",
      "clinvar_submissions_summary": "null",
      "phenotype_combined": "not provided",
      "pathogenicity_classification_combined": "Uncertain significance",
      "custom_annotations": null
    }
  ],
  "message": null
}