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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: 22-28696950-T-C (hg38)

Bash / cURL Example

bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=22&pos=28696950&ref=T&alt=C&genome=hg38&allGenes=true"

API Response

json
{
  "variants": [
    {
      "chr": "22",
      "pos": 28696950,
      "ref": "T",
      "alt": "C",
      "effect": "missense_variant",
      "transcript": "ENST00000404276.6",
      "consequences": [
        {
          "aa_ref": "K",
          "aa_alt": "R",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 10,
          "exon_rank_end": null,
          "exon_count": 15,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "CHEK2",
          "gene_hgnc_id": 16627,
          "hgvs_c": "c.1046A>G",
          "hgvs_p": "p.Lys349Arg",
          "transcript": "NM_007194.4",
          "protein_id": "NP_009125.1",
          "transcript_support_level": null,
          "aa_start": 349,
          "aa_end": null,
          "aa_length": 543,
          "cds_start": 1046,
          "cds_end": null,
          "cds_length": 1632,
          "cdna_start": 1104,
          "cdna_end": null,
          "cdna_length": 1844,
          "mane_select": "ENST00000404276.6",
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "K",
          "aa_alt": "R",
          "canonical": true,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 10,
          "exon_rank_end": null,
          "exon_count": 15,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "CHEK2",
          "gene_hgnc_id": 16627,
          "hgvs_c": "c.1046A>G",
          "hgvs_p": "p.Lys349Arg",
          "transcript": "ENST00000404276.6",
          "protein_id": "ENSP00000385747.1",
          "transcript_support_level": 1,
          "aa_start": 349,
          "aa_end": null,
          "aa_length": 543,
          "cds_start": 1046,
          "cds_end": null,
          "cds_length": 1632,
          "cdna_start": 1104,
          "cdna_end": null,
          "cdna_length": 1844,
          "mane_select": "NM_007194.4",
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "K",
          "aa_alt": "R",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 11,
          "exon_rank_end": null,
          "exon_count": 16,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "CHEK2",
          "gene_hgnc_id": 16627,
          "hgvs_c": "c.1175A>G",
          "hgvs_p": "p.Lys392Arg",
          "transcript": "ENST00000382580.6",
          "protein_id": "ENSP00000372023.2",
          "transcript_support_level": 1,
          "aa_start": 392,
          "aa_end": null,
          "aa_length": 586,
          "cds_start": 1175,
          "cds_end": null,
          "cds_length": 1761,
          "cdna_start": 1251,
          "cdna_end": null,
          "cdna_length": 1971,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "K",
          "aa_alt": "R",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 8,
          "exon_rank_end": null,
          "exon_count": 13,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "CHEK2",
          "gene_hgnc_id": 16627,
          "hgvs_c": "c.845A>G",
          "hgvs_p": "p.Lys282Arg",
          "transcript": "ENST00000402731.6",
          "protein_id": "ENSP00000384835.2",
          "transcript_support_level": 1,
          "aa_start": 282,
          "aa_end": null,
          "aa_length": 476,
          "cds_start": 845,
          "cds_end": null,
          "cds_length": 1431,
          "cdna_start": 851,
          "cdna_end": null,
          "cdna_length": 1591,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "K",
          "aa_alt": "R",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 7,
          "exon_rank_end": null,
          "exon_count": 12,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "CHEK2",
          "gene_hgnc_id": 16627,
          "hgvs_c": "c.773A>G",
          "hgvs_p": "p.Lys258Arg",
          "transcript": "ENST00000403642.5",
          "protein_id": "ENSP00000384919.1",
          "transcript_support_level": 1,
          "aa_start": 258,
          "aa_end": null,
          "aa_length": 452,
          "cds_start": 773,
          "cds_end": null,
          "cds_length": 1359,
          "cdna_start": 773,
          "cdna_end": null,
          "cdna_length": 1359,
          "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": 11,
          "exon_rank_end": null,
          "exon_count": 16,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "CHEK2",
          "gene_hgnc_id": 16627,
          "hgvs_c": "n.*536A>G",
          "hgvs_p": null,
          "transcript": "ENST00000416671.5",
          "protein_id": "ENSP00000402225.1",
          "transcript_support_level": 1,
          "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": 2560,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": false,
          "protein_coding": false,
          "strand": false,
          "consequences": [
            "3_prime_UTR_variant"
          ],
          "exon_rank": 11,
          "exon_rank_end": null,
          "exon_count": 16,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "CHEK2",
          "gene_hgnc_id": 16627,
          "hgvs_c": "n.*536A>G",
          "hgvs_p": null,
          "transcript": "ENST00000416671.5",
          "protein_id": "ENSP00000402225.1",
          "transcript_support_level": 1,
          "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": 2560,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "K",
          "aa_alt": "R",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 11,
          "exon_rank_end": null,
          "exon_count": 16,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "CHEK2",
          "gene_hgnc_id": 16627,
          "hgvs_c": "c.1175A>G",
          "hgvs_p": "p.Lys392Arg",
          "transcript": "NM_001005735.3",
          "protein_id": "NP_001005735.1",
          "transcript_support_level": null,
          "aa_start": 392,
          "aa_end": null,
          "aa_length": 586,
          "cds_start": 1175,
          "cds_end": null,
          "cds_length": 1761,
          "cdna_start": 1233,
          "cdna_end": null,
          "cdna_length": 1974,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "K",
          "aa_alt": "R",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 11,
          "exon_rank_end": null,
          "exon_count": 16,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "CHEK2",
          "gene_hgnc_id": 16627,
          "hgvs_c": "c.1139A>G",
          "hgvs_p": "p.Lys380Arg",
          "transcript": "NM_001438293.1",
          "protein_id": "NP_001425222.1",
          "transcript_support_level": null,
          "aa_start": 380,
          "aa_end": null,
          "aa_length": 574,
          "cds_start": 1139,
          "cds_end": null,
          "cds_length": 1725,
          "cdna_start": 1197,
          "cdna_end": null,
          "cdna_length": 1938,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "K",
          "aa_alt": "R",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 11,
          "exon_rank_end": null,
          "exon_count": 16,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "CHEK2",
          "gene_hgnc_id": 16627,
          "hgvs_c": "c.1046A>G",
          "hgvs_p": "p.Lys349Arg",
          "transcript": "ENST00000405598.5",
          "protein_id": "ENSP00000386087.1",
          "transcript_support_level": 5,
          "aa_start": 349,
          "aa_end": null,
          "aa_length": 543,
          "cds_start": 1046,
          "cds_end": null,
          "cds_length": 1632,
          "cdna_start": 1238,
          "cdna_end": null,
          "cdna_length": 1959,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "K",
          "aa_alt": "R",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 11,
          "exon_rank_end": null,
          "exon_count": 16,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "CHEK2",
          "gene_hgnc_id": 16627,
          "hgvs_c": "c.1046A>G",
          "hgvs_p": "p.Lys349Arg",
          "transcript": "ENST00000650281.1",
          "protein_id": "ENSP00000497000.1",
          "transcript_support_level": null,
          "aa_start": 349,
          "aa_end": null,
          "aa_length": 543,
          "cds_start": 1046,
          "cds_end": null,
          "cds_length": 1632,
          "cdna_start": 1206,
          "cdna_end": null,
          "cdna_length": 1923,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "K",
          "aa_alt": "R",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 9,
          "exon_rank_end": null,
          "exon_count": 14,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "CHEK2",
          "gene_hgnc_id": 16627,
          "hgvs_c": "c.845A>G",
          "hgvs_p": "p.Lys282Arg",
          "transcript": "NM_001349956.3",
          "protein_id": "NP_001336885.1",
          "transcript_support_level": null,
          "aa_start": 282,
          "aa_end": null,
          "aa_length": 476,
          "cds_start": 845,
          "cds_end": null,
          "cds_length": 1431,
          "cdna_start": 903,
          "cdna_end": null,
          "cdna_length": 1644,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "K",
          "aa_alt": "R",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 6,
          "exon_rank_end": null,
          "exon_count": 11,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "CHEK2",
          "gene_hgnc_id": 16627,
          "hgvs_c": "c.386A>G",
          "hgvs_p": "p.Lys129Arg",
          "transcript": "ENST00000464581.6",
          "protein_id": "ENSP00000483777.2",
          "transcript_support_level": 2,
          "aa_start": 129,
          "aa_end": null,
          "aa_length": 323,
          "cds_start": 386,
          "cds_end": null,
          "cds_length": 972,
          "cdna_start": 398,
          "cdna_end": null,
          "cdna_length": 1138,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "K",
          "aa_alt": "R",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 11,
          "exon_rank_end": null,
          "exon_count": 16,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "CHEK2",
          "gene_hgnc_id": 16627,
          "hgvs_c": "c.383A>G",
          "hgvs_p": "p.Lys128Arg",
          "transcript": "NM_001257387.3",
          "protein_id": "NP_001244316.1",
          "transcript_support_level": null,
          "aa_start": 128,
          "aa_end": null,
          "aa_length": 322,
          "cds_start": 383,
          "cds_end": null,
          "cds_length": 969,
          "cdna_start": 1218,
          "cdna_end": null,
          "cdna_length": 1959,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "K",
          "aa_alt": "R",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 9,
          "exon_rank_end": null,
          "exon_count": 14,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "CHEK2",
          "gene_hgnc_id": 16627,
          "hgvs_c": "c.383A>G",
          "hgvs_p": "p.Lys128Arg",
          "transcript": "NM_001437942.1",
          "protein_id": "NP_001424871.1",
          "transcript_support_level": null,
          "aa_start": 128,
          "aa_end": null,
          "aa_length": 322,
          "cds_start": 383,
          "cds_end": null,
          "cds_length": 969,
          "cdna_start": 779,
          "cdna_end": null,
          "cdna_length": 1520,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "K",
          "aa_alt": "R",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 9,
          "exon_rank_end": null,
          "exon_count": 14,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "CHEK2",
          "gene_hgnc_id": 16627,
          "hgvs_c": "c.383A>G",
          "hgvs_p": "p.Lys128Arg",
          "transcript": "ENST00000425190.7",
          "protein_id": "ENSP00000390244.2",
          "transcript_support_level": 5,
          "aa_start": 128,
          "aa_end": null,
          "aa_length": 322,
          "cds_start": 383,
          "cds_end": null,
          "cds_length": 969,
          "cdna_start": 770,
          "cdna_end": null,
          "cdna_length": 1510,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "K",
          "aa_alt": "R",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 7,
          "exon_rank_end": null,
          "exon_count": 12,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "CHEK2",
          "gene_hgnc_id": 16627,
          "hgvs_c": "c.383A>G",
          "hgvs_p": "p.Lys128Arg",
          "transcript": "ENST00000649563.1",
          "protein_id": "ENSP00000496928.1",
          "transcript_support_level": null,
          "aa_start": 128,
          "aa_end": null,
          "aa_length": 322,
          "cds_start": 383,
          "cds_end": null,
          "cds_length": 969,
          "cdna_start": 492,
          "cdna_end": null,
          "cdna_length": 1224,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "K",
          "aa_alt": "R",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 5,
          "exon_rank_end": null,
          "exon_count": 10,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "CHEK2",
          "gene_hgnc_id": 16627,
          "hgvs_c": "c.275A>G",
          "hgvs_p": "p.Lys92Arg",
          "transcript": "ENST00000434810.5",
          "protein_id": "ENSP00000416721.1",
          "transcript_support_level": 3,
          "aa_start": 92,
          "aa_end": null,
          "aa_length": 275,
          "cds_start": 275,
          "cds_end": null,
          "cds_length": 828,
          "cdna_start": 277,
          "cdna_end": null,
          "cdna_length": 984,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "K",
          "aa_alt": "R",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 11,
          "exon_rank_end": null,
          "exon_count": 16,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "CHEK2",
          "gene_hgnc_id": 16627,
          "hgvs_c": "c.1205A>G",
          "hgvs_p": "p.Lys402Arg",
          "transcript": "XM_011529839.3",
          "protein_id": "XP_011528141.1",
          "transcript_support_level": null,
          "aa_start": 402,
          "aa_end": null,
          "aa_length": 596,
          "cds_start": 1205,
          "cds_end": null,
          "cds_length": 1791,
          "cdna_start": 2748,
          "cdna_end": null,
          "cdna_length": 3488,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "K",
          "aa_alt": "R",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 11,
          "exon_rank_end": null,
          "exon_count": 16,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "CHEK2",
          "gene_hgnc_id": 16627,
          "hgvs_c": "c.1169A>G",
          "hgvs_p": "p.Lys390Arg",
          "transcript": "XM_017028560.2",
          "protein_id": "XP_016884049.1",
          "transcript_support_level": null,
          "aa_start": 390,
          "aa_end": null,
          "aa_length": 584,
          "cds_start": 1169,
          "cds_end": null,
          "cds_length": 1755,
          "cdna_start": 1228,
          "cdna_end": null,
          "cdna_length": 1968,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "K",
          "aa_alt": "R",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 10,
          "exon_rank_end": null,
          "exon_count": 15,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "CHEK2",
          "gene_hgnc_id": 16627,
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      ],
      "gene_symbol": "CHEK2",
      "gene_hgnc_id": 16627,
      "dbsnp": "rs1235802399",
      "frequency_reference_population": 0.0000012395583,
      "hom_count_reference_population": 0,
      "allele_count_reference_population": 2,
      "gnomad_exomes_af": 6.8432e-7,
      "gnomad_genomes_af": 0.00000657142,
      "gnomad_exomes_ac": 1,
      "gnomad_genomes_ac": 1,
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      "gnomad_genomes_homalt": 0,
      "gnomad_mito_homoplasmic": null,
      "gnomad_mito_heteroplasmic": null,
      "computational_score_selected": 0.9662373065948486,
      "computational_prediction_selected": "Pathogenic",
      "computational_source_selected": "MetaRNN",
      "splice_score_selected": 0.009999999776482582,
      "splice_prediction_selected": "Benign",
      "splice_source_selected": "max_spliceai",
      "revel_score": 0.91,
      "revel_prediction": "Pathogenic",
      "alphamissense_score": 0.9255,
      "alphamissense_prediction": null,
      "bayesdelnoaf_score": 0.43,
      "bayesdelnoaf_prediction": "Pathogenic",
      "phylop100way_score": 6.288,
      "phylop100way_prediction": "Uncertain_significance",
      "spliceai_max_score": 0.01,
      "spliceai_max_prediction": "Benign",
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      "mitotip_score": null,
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      "acmg_score": 8,
      "acmg_classification": "Likely_pathogenic",
      "acmg_criteria": "PM1,PM2,PP3_Strong",
      "acmg_by_gene": [
        {
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          "benign_score": 0,
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          "criteria": [
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            "PP3_Strong"
          ],
          "verdict": "Likely_pathogenic",
          "transcript": "ENST00000404276.6",
          "gene_symbol": "CHEK2",
          "hgnc_id": 16627,
          "effects": [
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          "inheritance_mode": "AD",
          "hgvs_c": "c.1046A>G",
          "hgvs_p": "p.Lys349Arg"
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      ],
      "clinvar_disease": "Familial cancer of breast,Hereditary cancer-predisposing syndrome",
      "clinvar_classification": "Uncertain significance",
      "clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
      "clinvar_submissions_summary": "US:2",
      "phenotype_combined": "Familial cancer of breast|Hereditary cancer-predisposing syndrome",
      "pathogenicity_classification_combined": "Uncertain significance",
      "custom_annotations": null
    }
  ],
  "message": null
}